diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 7fa6ef7..e4601c8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -8,41 +8,28 @@ on: pull_request: branches: - main - # run once a week + # run once a week schedule: - cron: "0 0 * * *" - workflow_dispatch: + workflow_dispatch: jobs: GenBank: runs-on: ubuntu-latest + container: colebrookson/virion:latest steps: - uses: actions/checkout@v3 - - uses: gautamkrishnar/keepalive-workflow@v1 - - name: Setup Julia - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v1 with: version: 1.7 - - name: Julia dependencies (DF) - run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add("CSV"); Pkg.add("DataFrames")' - - name: NCBITaxonomy (version from MAIN branch!) - run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add(PackageSpec(name="NCBITaxonomy", rev="main"))' - - name: Setup R - uses: r-lib/actions/setup-r@v2 - - name: Libraries for tidyverse - run: sudo apt-get install -y libharfbuzz-dev libfribidi-dev - - name: dependencies!!!! + - name: Download GenBank run: | - sudo apt-get install libcurl4-openssl-dev libarchive-dev - sudo Rscript -e 'install.packages(c("taxize", "tidyverse", "RCurl", "readr", "vroom", "magrittr", "fs", "data.table", "zip", "rglobi", "lubridate", "R.utils"), repos = "http://cran.us.r-project.org")' - - name: Download GenBank - run: | - Rscript -e 'source("Code/02_1a_Download GenBank.R")' + Rscript -e 'source("Code/02_1a_Download GenBank.R")' - name: Digest GenBank run: | Rscript -e 'source("Code/02_1b_Digest GenBank.R")' - name: Format GenBank run: | - Rscript -e 'source("Code/02_1c_Format GenBank.R")' + Rscript -e 'source("Code/02_1c_Format GenBank.R")' - name: Save artifacts uses: actions/upload-artifact@v2 with: @@ -50,25 +37,9 @@ jobs: path: Intermediate/Formatted/GenbankFormatted.csv.gz Globi: runs-on: ubuntu-latest + container: colebrookson/virion:latest steps: - uses: actions/checkout@v3 - - name: Setup R - uses: r-lib/actions/setup-r@v2 - - name: Libraries for tidyverse - run: sudo apt-get install -y libharfbuzz-dev libfribidi-dev - - name: dependencies!!!! - run: | - sudo apt-get install libcurl4-openssl-dev libarchive-dev - sudo Rscript -e 'install.packages(c("taxize", "tidyverse", "RCurl", "readr", "vroom", "magrittr", "fs", "data.table", "zip", "devtools", "lubridate"), repos = "http://cran.us.r-project.org")' - sudo Rscript -e 'devtools::install_github("ropensci/rglobi")' - - name: Setup Julia - uses: julia-actions/setup-julia@v1 - with: - version: 1.7 - - name: Julia dependencies (DF) - run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add("CSV"); Pkg.add("DataFrames")' - - name: NCBITaxonomy (version from MAIN branch!) - run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add(PackageSpec(name="NCBITaxonomy", rev="main"))' - name: Download Globi run: | Rscript -e 'source("Code/02_3a_Download GLOBI.R")' @@ -85,15 +56,10 @@ jobs: path: Intermediate/Formatted/GLOBIFormatted.csv Finish: runs-on: ubuntu-latest + container: colebrookson/virion:latest needs: [GenBank, Globi] steps: - uses: actions/checkout@v3 - - name: Setup R - uses: r-lib/actions/setup-r@v2 - - name: dependencies!!! - run: | - sudo apt-get install libcurl4-openssl-dev libarchive-dev libharfbuzz-dev libfribidi-dev - sudo Rscript -e 'install.packages(c("taxize", "tidyverse", "RCurl", "readr", "vroom", "magrittr", "fs", "data.table", "R.utils", "zip", "rglobi", "lubridate", "tidyft"), repos = "http://cran.us.r-project.org")' - name: Get GenBank uses: actions/download-artifact@v2 with: diff --git a/.gitignore b/.gitignore index 98f4470..6a9a298 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,4 @@ Intermediate/Formatted/GenbankFormatted.csv wc5/alt.bil wc5/alt.hdr Source/AllNuclMetadata.csv +Source/AllNuclMetadata.csv.gz diff --git a/Code/001_Julia functions.R b/Code/001_Julia functions.R index 7133469..b1d7cf2 100644 --- a/Code/001_Julia functions.R +++ b/Code/001_Julia functions.R @@ -1,10 +1,14 @@ -library(tidyverse) +#' Install Julia packages to use the functions for NCBI ======================== +#' +#' Here we use the JuliaCall library to get the funcitons we need + +# create install.ncbi() function =============================================== install.ncbi <- function() { - library(JuliaCall) - julia_setup() - julia_install_package_if_needed("NCBITaxonomy") - julia_install_package_if_needed("DataFrames") - julia_install_package_if_needed("CSV") - julia_install_package_if_needed("ProgressMeter") -} \ No newline at end of file + + # install the packages if needed + JuliaCall::julia_install_package_if_needed("NCBITaxonomy") + JuliaCall::julia_install_package_if_needed("DataFrames") + JuliaCall::julia_install_package_if_needed("CSV") + JuliaCall::julia_install_package_if_needed("ProgressMeter") +} diff --git a/Code/001_TaxizeFunctions.R b/Code/001_TaxizeFunctions.R index 74cc783..b1988a0 100644 --- a/Code/001_TaxizeFunctions.R +++ b/Code/001_TaxizeFunctions.R @@ -1,48 +1,80 @@ +#' Setting up the taxa functions +#' +#' There are a couple of functions that we need for the taxonomic stuff, we'll +#' do that and test it here -library(taxize) -library(tidyverse) -library(magrittr) - -virus.test <- c("Adeno-associated virus - 3", - "Adeno-associated virus 3B", - "Adenovirus predict_adv-20", - "A bad name") - - -host.test <- c("Equus caballus ferus", - "Homo sapiens", - "Hongus bongus", - "Chiroptera", - "Mus", - "Bacillus anthracis") +# functions ==================================================================== +#' mutate_cond +#' +#' @description a base R / dplyr mashup to do some data manipulation +#' +#' @param .data implied data object that we need +#' @param condition the condition that we're checking +#' @param envir note that this needs access to the parent set of call stacks +#' +#' @return .data mutate_cond <- function(.data, condition, ..., envir = parent.frame()) { condition <- eval(substitute(condition), .data, envir) .data[condition, ] <- .data[condition, ] %>% dplyr::mutate(...) .data } - +#' hdict() +#' +#' @description dictionary function for the host species - +#' using the names from the parent object, construct a new +#' dataframe that has all the relevant taxonomic variables split out into +#' new columns for easier presentation +#' +#' @param names vector of names of the object +#' +#' @return dataframe after all taxonomic operations hdict <- function(names) { + + # first deal with the names and get rid of every misplaced prefix names.orig <- names - names <- str_replace(names, " cf\\.","") - names <- str_replace(names, " sp\\.","") - names <- str_replace(names, " gen\\.","") - u <- get_uid(names, rank_filter = c("subspecies", "species", "genus", "family", "order", "class"), + names <- stringr::str_replace(names, " cf\\.","") + names <- stringr::str_replace(names, " sp\\.","") + names <- stringr::str_replace(names, " gen\\.","") + + # taxize function to get the UID codes for the taxonomic names + u <- taxize::get_uid(names, + rank_filter = c("subspecies", "species", "genus", + "family", "order", "class"), division_filter = "vertebrates", ask = FALSE) - c <- classification(u, batch_size = 10) - n <- !is.na(u) + + # tazise function to get the taxonomic hierarchy + c <- taxize::classification(u, batch_size = 10) + n <- !is.na(u) # keep the non-NA ones attributes(u) <- NULL - s <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="species")]], error = function(e) {NA})}), use.names = FALSE) - g <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="genus")]], error = function(e) {NA})}), use.names = FALSE) - f <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="family")]], error = function(e) {NA})}), use.names = FALSE) - o <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="order")]], error = function(e) {NA})}), use.names = FALSE) - c2 <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="class")]], error = function(e) {NA})}), use.names = FALSE) + # go through and get all of the separate taxonomic levels and extract them + # into vectors + s <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="species")]], + error = function(e) {NA} + )}), use.names = FALSE) + g <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="genus")]], + error = function(e) {NA})}), use.names = FALSE) + f <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="family")]], + error = function(e) {NA})}), use.names = FALSE) + o <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="order")]], + error = function(e) {NA})}), use.names = FALSE) + c2 <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="class")]], + error = function(e) {NA})}), use.names = FALSE) + + # extracting across all the levels here levels <- c("species", "genus", "family", "order", "class") - u <- unlist(lapply(c, function(x){tryCatch(last(na.omit(x[x$rank %in% levels,'id'])), - error = function(e) {NA})}), use.names = FALSE) + u <- unlist(lapply(c, function(x){ + tryCatch(last(na.omit(x[x$rank %in% levels,'id'])), + error = function(e) {NA})}), use.names = FALSE) + # turn the extracted vectors into a dataframe and return it data.frame(HostOriginal = names.orig, HostTaxID = u, HostNCBIResolved = n, @@ -50,25 +82,54 @@ hdict <- function(names) { HostGenus = g, HostFamily = f, HostOrder = o, - HostClass = c2) %>% mutate_cond(HostNCBIResolved == FALSE, Host = HostOriginal) %>% return() + HostClass = c2) %>% + mutate_cond(HostNCBIResolved == FALSE, Host = HostOriginal) %>% return() } +#' vdict() +#' +#' @description dictionary for the virus taxonomic names - +#' using the names from the parent object, construct a new +#' dataframe that has all the relevant taxonomic variables split out into +#' new columns for easier presentation +#' +#' @param names vector of names of the object +#' +#' @return dataframe after all taxonomic operations vdict <- function(names) { + + # first deal with the names and get rid of every misplaced prefix names.orig <- names - u <- get_uid(names, batch_size = 5, ask = FALSE) - c <- classification(u, batch_size = 5) + u <- taxize::get_uid(names, batch_size = 5, ask = FALSE) + c <- taxize::classification(u, batch_size = 5) n <- !is.na(u) attributes(u) <- NULL - s <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="species")]], error = function(e) {NA})}), use.names = FALSE) - g <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="genus")]], error = function(e) {NA})}), use.names = FALSE) - f <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="family")]], error = function(e) {NA})}), use.names = FALSE) - o <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="order")]], error = function(e) {NA})}), use.names = FALSE) - c2 <- unlist(lapply(c, function(x){tryCatch(x$name[[which(x$rank=="class")]], error = function(e) {NA})}), use.names = FALSE) + # go through and get all of the separate taxonomic levels and extract them + # into vectors + s <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="species")]], + error = function(e) {NA})}), use.names = FALSE) + g <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="genus")]], + error = function(e) {NA})}), use.names = FALSE) + f <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="family")]], + error = function(e) {NA})}), use.names = FALSE) + o <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="order")]], + error = function(e) {NA})}), use.names = FALSE) + c2 <- unlist(lapply(c, function(x){ + tryCatch(x$name[[which(x$rank=="class")]], + error = function(e) {NA})}), use.names = FALSE) + + # extracting across all the levels here levels <- c("species", "genus", "family", "order", "class") - u <- unlist(lapply(c, function(x){tryCatch(last(na.omit(x[x$rank %in% levels,'id'])), - error = function(e) {NA})}), use.names = FALSE) + u <- unlist(lapply(c, function(x){ + tryCatch(last(na.omit(x[x$rank %in% levels,'id'])), + error = function(e) {NA})}), use.names = FALSE) + # turn the extracted vectors into a dataframe and return it data.frame(VirusOriginal = names.orig, VirusTaxID = u, VirusNCBIResolved = n, @@ -76,70 +137,134 @@ vdict <- function(names) { VirusGenus = g, VirusFamily = f, VirusOrder = o, - VirusClass = c2) %>% mutate_cond(VirusNCBIResolved == FALSE, Virus = VirusOriginal) %>% return() + VirusClass = c2) %>% + mutate_cond(VirusNCBIResolved == FALSE, Virus = VirusOriginal) %>% return() } - +#' jhdict() +#' +#' @description dictionary for the host taxonomic names but with Julia - +#' using the names from the parent object, construct a new +#' dataframe that has all the relevant taxonomic variables split out into +#' new columns for easier presentation +#' +#' @param spnames vector of species names in the object +#' +#' @return dataframe after all both Julia and R operations jhdict <- function(spnames) { + + # turn this into a dataframe for ease raw <- data.frame(Name = spnames) - write_csv(raw, './Code/Code_Dev/TaxonomyTempIn.csv', eol = "\n") - system("julia --project Code/Code_Dev/host.jl") - clean <- read_csv("./Code/Code_Dev/TaxonomyTempOut.csv") - file.remove('./Code/Code_Dev/TaxonomyTempIn.csv') - file.remove('./Code/Code_Dev/TaxonomyTempOut.csv') + # this raw temp df is going to be passed to julia + readr::write_csv(raw, here::here("./Code/Code_Dev/TaxonomyTempIn.csv"), + eol = "\n") + + # ensure that the system() call is giving the whole path name of the file + system(paste0( + "julia --project ", + here::here("Code/Code_Dev/host.jl"))) # this is better for reproducing this + + # after Julia has worked read in the cleaned file and get rid of the tmp files + clean <- readr::read_csv(here::here("./Code/Code_Dev/TaxonomyTempOut.csv")) + file.remove(here::here("./Code/Code_Dev/TaxonomyTempIn.csv")) + file.remove(here::here("./Code/Code_Dev/TaxonomyTempOut.csv")) + + # the clean file needs to be sliced up + clean %<>% dplyr::group_by(Name) %>% + dplyr::slice(which.min(TaxId)) - clean %<>% group_by(Name) %>% - slice(which.min(TaxId)) - - clean %<>% rename(HostOriginal = Name, + # there's a renaming process to keep all the names of the df standard + clean %<>% dplyr::rename(HostOriginal = Name, HostTaxID = TaxId, Host = Species, HostGenus = Genus, HostFamily = Family, HostOrder = Order, HostClass = Class) %>% - mutate(HostNCBIResolved = TRUE) %>% - select(-Rank) + dplyr::mutate(HostNCBIResolved = TRUE) %>% + dplyr::select(-Rank) + # bad df is the one for which we don't have the NCBI resolved values bad <- data.frame(HostOriginal = spnames[!(spnames %in% clean$HostOriginal)], HostNCBIResolved = FALSE) - clean %<>% bind_rows(bad) %>% - select(HostOriginal, HostTaxID, HostNCBIResolved, Host, HostGenus, HostFamily, HostOrder, HostClass) + # keeping both parts, but also want the bad ones, but it's noted in the + # HostNCBIResolved column + clean %<>% dplyr::bind_rows(bad) %>% + dplyr::select(HostOriginal, HostTaxID, HostNCBIResolved, Host, + HostGenus, HostFamily, HostOrder, HostClass) return(clean) } - +#' jvdict() +#' +#' @description dictionary for the virus taxonomic names but with Julia - +#' using the names from the parent object, construct a new +#' dataframe that has all the relevant taxonomic variables split out into +#' new columns for easier presentation +#' +#' @param spnames vector of species names in the object +#' +#' @return dataframe after all both Julia and R operations jvdict <- function(spnames) { + + # turn this into a dataframe for ease raw <- data.frame(Name = spnames) - write_csv(raw, './Code/Code_Dev/TaxonomyTempIn.csv', eol = "\n") - system("julia --project Code/Code_Dev/virus.jl") - clean <- read_csv("./Code/Code_Dev/TaxonomyTempOut.csv") - file.remove('./Code/Code_Dev/TaxonomyTempIn.csv') - file.remove('./Code/Code_Dev/TaxonomyTempOut.csv') + # this raw temp df is going to be passed to julia + readr::write_csv(raw, here::here("./Code/Code_Dev/TaxonomyTempIn.csv"), + eol = "\n") + + # ensure that the system() call is giving the whole path name of the file + system(paste0( + "julia --project ", + here::here("Code/Code_Dev/virus.jl"))) # this is better for reproducing this - clean %<>% group_by(Name) %>% - slice(which.min(TaxId)) + # after Julia has worked read in the cleaned file and get rid of the tmp files + clean <- readr::read_csv(here::here("./Code/Code_Dev/TaxonomyTempOut.csv")) + file.remove(here::here("./Code/Code_Dev/TaxonomyTempIn.csv")) + file.remove(here::here("./Code/Code_Dev/TaxonomyTempOut.csv")) - clean %<>% rename(VirusOriginal = Name, + # there's a renaming process to keep all the names of the df standard + clean %<>% dplyr::group_by(Name) %>% + dplyr::slice(which.min(TaxId)) + + # there's a renaming process to keep all the names of the df standard + clean %<>% dplyr::rename(VirusOriginal = Name, VirusTaxID = TaxId, Virus = Species, VirusGenus = Genus, VirusFamily = Family, VirusOrder = Order, VirusClass = Class) %>% - mutate(VirusNCBIResolved = TRUE) %>% - select(-Rank) + dplyr::mutate(VirusNCBIResolved = TRUE) %>% + dplyr::select(-Rank) - bad <- data.frame(VirusOriginal = spnames[!(spnames %in% clean$VirusOriginal)], + # bad df is the one for which we don't have the NCBI resolved values + bad <- data.frame( + VirusOriginal = spnames[!(spnames %in% clean$VirusOriginal)], VirusNCBIResolved = FALSE) - clean %<>% bind_rows(bad) %>% - select(VirusOriginal, VirusTaxID, VirusNCBIResolved, Virus, VirusGenus, VirusFamily, VirusOrder, VirusClass) + # keeping both parts, but also want the bad ones, but it's noted in the + # HostNCBIResolved column + clean %<>% dplyr::bind_rows(bad) %>% + dplyr::select(VirusOriginal, VirusTaxID, VirusNCBIResolved, Virus, + VirusGenus, VirusFamily, VirusOrder, VirusClass) return(clean) } +# tests ======================================================================== + +virus.test <- c("Adeno-associated virus - 3", + "Adeno-associated virus 3B", + "Adenovirus predict_adv-20", + "A bad name") +host.test <- c("Equus caballus ferus", + "Homo sapiens", + "Hongus bongus", + "Chiroptera", + "Mus", + "Bacillus anthracis") diff --git a/Code/00_File_Template.R b/Code/00_File_Template.R new file mode 100644 index 0000000..f4efc36 --- /dev/null +++ b/Code/00_File_Template.R @@ -0,0 +1,13 @@ +# Set-up ======================================================================= + +#' have all the source calls etc in the top of the file + +# Section 1 ==================================================================== + +#' In each section, all code should be in as few chunks as possible and as much +#' in base code as possible (fewer dependency issues) + +# Last Section ================================================================= + +#' Ensure that any writing out of objects all happens at the end and that we +#' do any small tests here \ No newline at end of file diff --git a/Code/01_Generate Template.R b/Code/01_Generate Template.R index 2b73273..ca4c3c8 100644 --- a/Code/01_Generate Template.R +++ b/Code/01_Generate Template.R @@ -1,7 +1,9 @@ +#' Generate file template +#' +#' This file generates a dataframe of zero rows but 32 variables that has the +#' type coding for each variable that will be used later -library(tidyverse) -library(magrittr) - +# Generate example file ======================================================== temp <- data.frame(Host = character(), Virus = character(), HostTaxID = double(), @@ -36,4 +38,5 @@ temp <- data.frame(Host = character(), CollectionDay = double(), stringsAsFactors = FALSE) -write_csv(temp, "Intermediate/Template.csv") +# write file =================================================================== +readr::write_csv(temp, here::here("Intermediate/Template.csv")) diff --git a/Code/02_0_Format CLOVER.R b/Code/02_0_Format CLOVER.R index 1ce0963..7d85a12 100644 --- a/Code/02_0_Format CLOVER.R +++ b/Code/02_0_Format CLOVER.R @@ -1,9 +1,19 @@ +#' Format CLOVER +#' +#' Clover is a static file that comes from the clover database and you need to +#' read it in from that location + +# Set up ======================================================================= -library(tidyverse) library(magrittr) -library(lubridate) -clo <- read_csv("~/Github/clover/clover/clover_1.0_allpathogens/CLOVER_1.0_Viruses_AssociationsFlatFile.csv") + + +clo <- readr::read_csv(here::here(paste0( + "../clover/clover/clover_1.0_allpathogens/", + "CLOVER_1.0_Viruses_AssociationsFlatFile.csv"))) + +# template dataframe =========================================================== temp <- data.frame(Host = character(), Virus = character(), @@ -39,46 +49,50 @@ temp <- data.frame(Host = character(), CollectionDay = double(), stringsAsFactors = FALSE) +# do some cleaning on clover =================================================== + # This step should go away after Rory updates CLOVERT with the "sp." thing -if(!("HostGenus" %in% colnames(clo))) { clo %<>% mutate(HostGenus = word(Host, 1)) } +if(!("HostGenus" %in% colnames(clo))) { + clo %<>% dplyr::mutate(HostGenus = stringr::word(Host, 1)) } # This step should go away after Rory updates to remove CitationID if("CitationID" %in% colnames(clo)) { clo %>% - rowwise() %>% - mutate(NCBIAccession = ifelse(CitationIDType=='NCBI Nucleotide', CitationID, NA), + dplyr::rowwise() %>% + dplyr::mutate(NCBIAccession = + ifelse(CitationIDType=='NCBI Nucleotide', CitationID, NA), PMID = ifelse(CitationIDType=='PMID', CitationID, NA)) %>% - select(-c(CitationID, CitationIDType)) -> clo + dplyr::select(-c(CitationID, CitationIDType)) -> clo } -clo %<>% rename(Virus = "Pathogen", - VirusGenus = "PathogenGenus", - VirusFamily = "PathogenFamily", - VirusOrder = "PathogenOrder", - VirusClass = "PathogenClass", - DetectionOriginal = "DetectionMethodOriginal", - VirusNCBIResolved = "PathogenNCBIResolved", - VirusOriginal = "PathogenOriginal", - VirusTaxID = "PathogenTaxID") +# names need to be consistent +clo %<>% dplyr::rename(Virus = "Pathogen", + VirusGenus = "PathogenGenus", + VirusFamily = "PathogenFamily", + VirusOrder = "PathogenOrder", + VirusClass = "PathogenClass", + DetectionOriginal = "DetectionMethodOriginal", + VirusNCBIResolved = "PathogenNCBIResolved", + VirusOriginal = "PathogenOriginal", + VirusTaxID = "PathogenTaxID") -clo %<>% select(-c(PathogenType, - Detection_NotSpecified, - Detection_Serology, - Detection_Genetic, - Detection_Isolation)) +clo %<>% dplyr::select(-c(PathogenType, + Detection_NotSpecified, + Detection_Serology, + Detection_Genetic, + Detection_Isolation)) -clo %<>% mutate(NCBIAccession = as.character(NCBIAccession)) - -clo %<>% select(-ICTVRatified) - -# colnames(clo)[!(colnames(clo) %in% colnames(temp))] # Deleted check - -bind_rows(temp, clo) -> clo +clo %<>% dplyr::mutate(NCBIAccession = as.character(NCBIAccession)) +clo %<>% dplyr::select(-ICTVRatified) +clo <- dplyr::bind_rows(temp, clo) # Consistency steps: all lowercase names - -clo %<>% mutate_at(c("Host", "HostGenus", "HostFamily", "HostOrder", "HostClass", - "Virus", "VirusGenus", "VirusFamily", "VirusOrder", "VirusClass"), +clo %<>% dplyr::mutate_at(c("Host", "HostGenus", "HostFamily", "HostOrder", + "HostClass","Virus", "VirusGenus", "VirusFamily", + "VirusOrder", "VirusClass"), tolower) -write_csv(clo, 'Intermediate/Formatted/CLOVERFormatted.csv') +# write out ==================================================================== + +readr::write_csv(clo, + here::here("./Intermediate/Formatted/CLOVERFormatted.csv")) diff --git a/Code/02_1a_Download GenBank.R b/Code/02_1a_Download GenBank.R index 9c7599e..240412d 100644 --- a/Code/02_1a_Download GenBank.R +++ b/Code/02_1a_Download GenBank.R @@ -1,20 +1,27 @@ +#' Download GenBank +#' +#' GenBank is an updating resource so you have to pull it and this script does +#' that -library(RCurl) -library(readr) -library(R.utils) -library(tidyverse) -library(vroom) +# set up ======================================================================= -url = "https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/AllNuclMetadata.csv.gz" -d = tryCatch(download.file(url, destfile = "./Source/AllNuclMetadata.csv.gz"), error = function(e){-999}) -if(d == -999) { - while (d == -999){ - Sys.sleep(600) - d = tryCatch(download.file(url, destfile = "./Source/AllNuclMetadata.csv.gz"), error = function(e){-999}) - } -} +library(magrittr) -seq <- data.table::fread("./Source/AllNuclMetadata.csv.gz", - select = c("#Accession", "Release_Date", "Species", "Host", "Collection_Date")) -seq %>% rename(Accession = "#Accession") %>% - vroom_write("./Source/sequences.csv") +# download and process ========================================================= + +url = paste0("https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/", + "AllNuclMetadata.csv.gz") + +location <- here::here("./Source/") +system(paste0("wget ", url, " -P ", location)) + +# reading this in - use data.table +seq <- data.table::fread(here::here("./Source/AllNuclMetadata.csv.gz"), + select = c("#Accession", "Release_Date", "Species", + "Host", "Collection_Date")) +print("readin") +seq %<>% dplyr::rename(Accession = "#Accession") + +# write out ==================================================================== +vroom::vroom_write(seq, here::here("./Source/sequences.csv")) +print("written") diff --git a/Code/02_1b_Digest GenBank.R b/Code/02_1b_Digest GenBank.R index e92135f..f80d392 100644 --- a/Code/02_1b_Digest GenBank.R +++ b/Code/02_1b_Digest GenBank.R @@ -1,45 +1,67 @@ +#" GenBank digesting with NCBI +#" +#" There"s some cleaning to do, and that"s done here +#" -# 01_Setup #### +# set up ======================================================================= -rm(list = ls()) +library(magrittr) -library(tidyverse); library(taxize); library(magrittr); library(fs); library(zip); library(vroom) +# this is necessary for using the NCBI records of more than 10 rentrez::set_entrez_key("ec345b39079e565bdfa744c3ef0d4b03ba08") -if(!exists('vdict')) {source('Code/001_TaxizeFunctions.R')} -if(!exists('jvdict')) {source('Code/001_Julia functions.R')} +# get the functions to do all the dictionary stuff +source(here::here("./Code/001_TaxizeFunctions.R")) +source(here::here("./Code/001_Julia functions.R")) -if(!file.exists("Source/sequences.csv")){ - unzip("Source/GenBank.zip", exdir = 'Source') +if(!file.exists(here::here("./Source/sequences.csv"))){ + zip::unzip(here::here("./Source/GenBank.zip"), exdir = "Source") } -gb <- data.table::fread("Source/sequences.csv") %>% - as_tibble - -gb %>% pull(Host) %>% unique() %>% sort() -> host.list -host.table <- jhdict(host.list) -write_csv(host.table, 'Intermediate/GBHostTax.csv') - -gb %<>% rename(HostOriginal = "Host") %>% - left_join(host.table) %>% - filter(HostClass %in% c("Actinopteri", - "Actinopterygii", - "Amphibia", - "Aves", - "Chondrichthyes", - "Cladistia", - "Hyperoartia", - "Lepidosauria", - "Mammalia", - "Myxini", - "Reptilia") | HostOrder %in% c("Testudines", "Crocodylia")) - # Reptilia is defunct but left in case GLOBI has something on it or it's reinstituted or something weird - -gb %>% pull(Species) %>% unique() %>% sort() -> virus.list -virus.table <- jvdict(virus.list) -write_csv(virus.table, 'Intermediate/GBVirusTax.csv') - -gb %<>% rename(VirusOriginal = "Species") %>% - left_join(virus.table) - -vroom_write(gb, "Intermediate/Unformatted/GenBankUnformatted.csv.gz") +install.ncbi() + +gb <- data.table::fread(here::here("./Source/sequences.csv")) %>% + dplyr::as_tibble() + +# do the cleaning itself ======================================================= +host_vec <- gb %>% + dplyr::pull(Host) %>% + unique() %>% + sort() + +host_table <- jhdict(host_vec) +readr::write_csv(host_table, here::here("./Intermediate/GBHostTax.csv")) + +gb %<>% dplyr::rename(HostOriginal = "Host") %>% + dplyr::left_join(host_table) %>% + dplyr::filter(HostClass %in% c("Actinopteri", + "Amphibia", + "Aves", + "Chondrichthyes", + "Cladistia", + "Hyperoartia", + "Lepidosauria", + "Mammalia", + "Myxini", + "Reptilia") | HostOrder %in% + c("Testudines", "Crocodylia")) + # Reptilia is defunct but left in case GLOBI has something on it + # or it"s reinstituted or something weird + +# get vector of the species names +virus_vec <- gb %>% + dplyr::pull(Species) %>% + unique() %>% + sort() + +# get julia to help here +virus_table <- jvdict(virus_vec) + +gb %<>% dplyr::rename(VirusOriginal = "Species") %>% + dplyr::left_join(virus_table) + +# write files ================================================================== +vroom::vroom_write(gb, here::here( + "./Intermediate/Unformatted/GenBankUnformatted.csv.gz")) +readr::write_csv(virus_table, here::here("./Intermediate/GBVirusTax.csv")) + diff --git a/Code/02_1c_Format GenBank.R b/Code/02_1c_Format GenBank.R index 964345e..14bf205 100644 --- a/Code/02_1c_Format GenBank.R +++ b/Code/02_1c_Format GenBank.R @@ -1,7 +1,17 @@ -# set up -library(tidyverse); library(magrittr); library(vroom); library(data.table) + +#" GenBank formatting to play nice with all the other pieces +#" +#" Make sure that all the structure matches up with the structure we"ve laid +#" out + +# set up ======================================================================= + +library(magrittr) + if(!exists('vdict')) {source('Code/001_TaxizeFunctions.R')} +print("vdict") if(!exists('jvdict')) {source('Code/001_Julia functions.R')} +print("jvdict") temp <- data.frame(Host = character(), Virus = character(), @@ -40,17 +50,16 @@ temp <- data.frame(Host = character(), # Attaching GenBank gb <- vroom::vroom("Intermediate/Unformatted/GenBankUnformatted.csv.gz") print("rows in genbank as of this run is: ", nrow(gb)) + gb %<>% dplyr::rename(NCBIAccession = 'Accession') %>% dplyr::rename(Release_Date = Release_Date) %>% # not sure what this is doing? - - # really don't know why we want or need this here????? dplyr::mutate_at("Release_Date", ~.x %>% # Modifying date column to make sense stringr::str_split("T") %>% # Splitting at this midpoint purrr::map_chr(1) %>% # Taking the first component lubridate::ymd() # Coding as YMD (shouldn't throw errors) ) -print("renamed") +print("renamed") gb[, c(paste0("Collection", c("Year", "Month", "Day")))] <- data.table::tstrsplit(gb$Collection_Date, "-", @@ -75,14 +84,14 @@ gb %<>% dplyr::mutate_at(dplyr::vars(tidyselect::matches("Year|Month|Day")), as.numeric) %>% dplyr::mutate(HostFlagID = stringr::str_detect(HostOriginal, "cf."), - Database = "GenBank", - DatabaseVersion = "Aug2021FlatFile", - # Choice to call Nucleotide all sequence and not isolation is - # potentially problematic - revisit - DetectionMethod = "PCR/Sequencing", - # Just to keep separate from EID2 Nucleotide entries # Fix - # the HostSynonyms at the 01 import stage - DetectionOriginal = "GenBank") + Database = "GenBank", + DatabaseVersion = "Aug2021FlatFile", + # Choice to call Nucleotide all sequence and not isolation is + # potentially problematic - revisit + DetectionMethod = "PCR/Sequencing", + # Just to keep separate from EID2 Nucleotide entries # Fix + # the HostSynonyms at the 01 import stage + DetectionOriginal = "GenBank") print("mutated") gb %<>% dplyr::mutate(VirusTaxID = as.numeric(VirusTaxID)) %>% @@ -94,11 +103,13 @@ gb %<>% tolower) -print("mutate at") +print("mutate at"); gc() # write intermediate file vroom::vroom_write(gb, "Intermediate/Formatted/GenbankFormatted.csv.gz") print("written") +# unused benchmarking ========================================================== + ## little benchmarking # microbenchmark::microbenchmark( # data.table = { @@ -111,14 +122,16 @@ print("written") # c("Year", "Month", "Day"))) # }, # tidyr = { -# gb %>% +# gb %>% # # known that the collection date is a string and many observations don't -# # have year or month values, just the year, so many of these will turn up +# # have year or month values just the year, so many of these will turn up # # as missing -# tidyr::separate(Collection_Date, sep = "-", -# into = paste0("Collection", c("Year", "Month", "Day"))) %>% -# tidyr::separate(Release_Date, sep = "-", -# into = paste0("Release", c("Year", "Month", "Day"))) +# tidyr::separate( +# Collection_Date, sep = "-", +# into = paste0("Collection", c("Year", "Month", "Day"))) %>% +# tidyr::separate( +# Release_Date, sep = "-", +# into = paste0("Release", c("Year", "Month", "Day"))) # }, # times = 100 # ) diff --git a/Code/02_2a_Digest PREDICT.R b/Code/02_2a_Digest PREDICT.R index 6335420..dddfea1 100644 --- a/Code/02_2a_Digest PREDICT.R +++ b/Code/02_2a_Digest PREDICT.R @@ -30,26 +30,26 @@ predict.raw %>% TRUE, FALSE)) %>% mutate(Host = str_replace(Host, " \\*",""), - Host = str_replace(Host, "cf. ","")) %>% - + Host = str_replace(Host, "cf. ","")) %>% + # Back up the virus names before doing anything else mutate(VirusOriginal = Virus) %>% rename(VirusIntermediate = "Virus") %>% - + # Remove "Strain of" from virus names mutate(VirusIntermediate = str_replace(VirusIntermediate, "strain of ","")) %>% # Fix the date information into the right format mutate(CollectionYear = year(Date), - CollectionMonth = month(Date), - CollectionDay = day(Date), - ReleaseYear = 2021, - ReleaseMonth = 3, - ReleaseDay = 9, - Database = "PREDICT", - DatabaseVersion = "March92021FlatFile", - DetectionMethod = "PCR/Sequencing") %>% + CollectionMonth = month(Date), + CollectionDay = day(Date), + ReleaseYear = 2021, + ReleaseMonth = 3, + ReleaseDay = 9, + Database = "PREDICT", + DatabaseVersion = "March92021FlatFile", + DetectionMethod = "PCR/Sequencing") %>% select(-Date) -> predict # First, let's fix some typos and such @@ -59,23 +59,23 @@ predict %>% rowwise() %>% mutate(VirusIntermediate = strsplit(VirusIntermediate, predict %>% rowwise() %>% mutate(VirusIntermediate = strsplit(VirusIntermediate, split=", partial subtype")[[1]][1]) -> predict predict %>% mutate(VirusIntermediate = recode(VirusIntermediate, !!!c("Yellow Fever" = "Yellow fever virus", - "Dengue virus serotype 1" = "Dengue virus", - "Dengue virus serotype 2" = "Dengue virus", - "Dengue virus serotype 3" = "Dengue virus", - "Dengue virus serotype 4" = "Dengue virus", - "Influenza A" = "Influenza A virus", - "Influenza B" = "Influenza B virus", - "Human BK Polyomavirus" = "Human polyomavirus 1", - "Porcine Parainfluenzavirus 1" = "Porcine parainfluenza virus", - "Human Parainfluenzavirus 1" = "Human respirovirus 1", - "Human Parainfluenzavirus 3" = "Human respirovirus 3", - "Human Parainfluenzavirus 2" = "Human rubulavirus 2", - "Human Parainfluenzavirus 4" = "Human rubulavirus 4", - "Marburg Virus " = "Marburg marburgvirus", - "MERS-like Coronovirus" = "Bat MERS-like coronavirus", - "Monkey pox" = "Monkeypox virus", - "Morogoro virus" = "Morogoro mammarenavirus", - "SFVHpi" = "Simian foamy virus"))) -> predict + "Dengue virus serotype 1" = "Dengue virus", + "Dengue virus serotype 2" = "Dengue virus", + "Dengue virus serotype 3" = "Dengue virus", + "Dengue virus serotype 4" = "Dengue virus", + "Influenza A" = "Influenza A virus", + "Influenza B" = "Influenza B virus", + "Human BK Polyomavirus" = "Human polyomavirus 1", + "Porcine Parainfluenzavirus 1" = "Porcine parainfluenza virus", + "Human Parainfluenzavirus 1" = "Human respirovirus 1", + "Human Parainfluenzavirus 3" = "Human respirovirus 3", + "Human Parainfluenzavirus 2" = "Human rubulavirus 2", + "Human Parainfluenzavirus 4" = "Human rubulavirus 4", + "Marburg Virus " = "Marburg marburgvirus", + "MERS-like Coronovirus" = "Bat MERS-like coronavirus", + "Monkey pox" = "Monkeypox virus", + "Morogoro virus" = "Morogoro mammarenavirus", + "SFVHpi" = "Simian foamy virus"))) -> predict # Now: the taxonomy. First: generate a list of every PREDICT_ virus name @@ -146,7 +146,7 @@ predict %>% pull(VirusIntermediate) %>% str_subset("PREDICT", negate = TRUE) %>% ncbi.tax <- vdict(ncbi.names) ncbi.tax %<>% rename(VirusIntermediate = "VirusOriginal") - + # Add some guardrails for (i in 1:nrow(ncbi.tax)) { @@ -259,49 +259,450 @@ for(i in 1:nrow(predict)) { acc <- word(predict$Accession[i], 1, sep = ", ") tax <- tryCatch(tax <- entrez_summary(db="nuccore", id = acc)$taxid, error = function(e) {NA}) if(!is.na(tax)) { - ncbi.high <- taxize::classification(tax, db = "ncbi") - if(!is.na(ncbi.high[[1]][1])){ - if(!(any(str_detect(ncbi.high[[1]]$name[which(ncbi.high[[1]]$rank=='species')], c('unidentified', 'unclassified', 'sp.'))))) { - predict$VirusNCBIResolved[i] <- TRUE - if("species" %in% ncbi.high[[1]]$rank) {predict$Virus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='species'), 'name']} - if("genus" %in% ncbi.high[[1]]$rank) {predict$VirusGenus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='genus'), 'name']} - if("family" %in% ncbi.high[[1]]$rank) {predict$VirusFamily[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='family'), 'name']} - if("order" %in% ncbi.high[[1]]$rank) {predict$VirusOrder[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='order'), 'name']} - if("class" %in% ncbi.high[[1]]$rank) {predict$VirusClass[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='class'), 'name']} - - levels <- c("species", "genus", "family", "order", "class") - u <- last(ncbi.high[[1]][ncbi.high[[1]]$rank %in% levels,'id']) - predict$VirusTaxID[i] <- u - - print(ncbi.high) + ncbi.high <- taxize::classification(tax, db = "ncbi") + if(!is.na(ncbi.high[[1]][1])){ + if(!(any(str_detect(ncbi.high[[1]]$name[which(ncbi.high[[1]]$rank=='species')], c('unidentified', 'unclassified', 'sp.'))))) { + predict$VirusNCBIResolved[i] <- TRUE + if("species" %in% ncbi.high[[1]]$rank) {predict$Virus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='species'), 'name']} + if("genus" %in% ncbi.high[[1]]$rank) {predict$VirusGenus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='genus'), 'name']} + if("family" %in% ncbi.high[[1]]$rank) {predict$VirusFamily[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='family'), 'name']} + if("order" %in% ncbi.high[[1]]$rank) {predict$VirusOrder[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='order'), 'name']} + if("class" %in% ncbi.high[[1]]$rank) {predict$VirusClass[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='class'), 'name']} + + levels <- c("species", "genus", "family", "order", "class") + u <- last(ncbi.high[[1]][ncbi.high[[1]]$rank %in% levels,'id']) + predict$VirusTaxID[i] <- u + + print(ncbi.high) + } } + } + } +} + + + + + + + +#" Predict digestion +#" +#" Predict is also a flat file that we pull in and deal with ourselves + +# set up ======================================================================= + +library(magrittr) + +if(!exists("jncbi")) {source(here::here("./Code/001_Julia functions.R"))} +if(!exists("vdict")) {source(here::here("./Code/001_TaxizeFunctions.R"))} + +predict_raw <- readr::read_csv(here::here("../ept/PredictData (2).csv")) +rentrez::set_entrez_key("ec345b39079e565bdfa744c3ef0d4b03ba08") + +# formatting predict =========================================================== + +predict <- predict_raw %>% + # Drop long lats, number of records + dplyr::select(`Sample Date`, + `Species Scientific Name Based on Field Morphology`, + Virus, + `Genbank #`) %>% + # Some minor variable recodings + dplyr::rename(Date = `Sample Date`, + Host = `Species Scientific Name Based on Field Morphology`, + Accession = `Genbank #`) %>% + # group_by_at(vars(-Accession)) %>% + # summarize(Accession = str_c(Accession, collapse = ", ")) %>% + unique() %>% + # The below step deals with flagged host names and "cf." names equally + dplyr::mutate(HostFlagID = ifelse( + (stringr::str_detect(Host, "\\*") | stringr::str_detect(Host,"cf.")), + TRUE, + FALSE)) %>% + dplyr::mutate(Host = stringr::str_replace(Host, " \\*",""), + Host = stringr::str_replace(Host, "cf. ","")) %>% + # Back up the virus names before doing anything else + dplyr::mutate(VirusOriginal = Virus) %>% + dplyr::rename(VirusIntermediate = "Virus") %>% + # Remove "Strain of" from virus names + dplyr::mutate(VirusIntermediate = + stringr::str_replace(VirusIntermediate, "strain of ","")) %>% + # Fix the date information into the right format + dplyr::mutate(CollectionYear = lubridate::year(Date), + CollectionMonth = lubridate::month(Date), + CollectionDay = lubridate::day(Date), + ReleaseYear = 2021, + ReleaseMonth = 3, + ReleaseDay = 9, + Database = "PREDICT", + DatabaseVersion = "March92021FlatFile", + DetectionMethod = "PCR/Sequencing") %>% + dplyr::select(-Date) + +## typos ======================================================================= + +predict %<>% + dplyr::rowwise() %>% + dplyr::mutate(VirusIntermediate = + strsplit(VirusIntermediate, split="\\(")[[1]][1]) +predict %<>% + dplyr::rowwise() %>% + dplyr::mutate(VirusIntermediate = + strsplit(VirusIntermediate, split=", subtype")[[1]][1]) +predict %<>% + dplyr::rowwise() %>% + dplyr::mutate(VirusIntermediate = + strsplit(VirusIntermediate, + split=", partial subtype")[[1]][1]) + +predict %<>% + dplyr::mutate(VirusIntermediate = dplyr::recode( + VirusIntermediate, + !!!c("Yellow Fever" = "Yellow fever virus", + "Dengue virus serotype 1" = "Dengue virus", + "Dengue virus serotype 2" = "Dengue virus", + "Dengue virus serotype 3" = "Dengue virus", + "Dengue virus serotype 4" = "Dengue virus", + "Influenza A" = "Influenza A virus", + "Influenza B" = "Influenza B virus", + "Human BK Polyomavirus" = "Human polyomavirus 1", + "Porcine Parainfluenzavirus 1" = "Porcine parainfluenza virus", + "Human Parainfluenzavirus 1" = "Human respirovirus 1", + "Human Parainfluenzavirus 3" = "Human respirovirus 3", + "Human Parainfluenzavirus 2" = "Human rubulavirus 2", + "Human Parainfluenzavirus 4" = "Human rubulavirus 4", + "Marburg Virus " = "Marburg marburgvirus", + "MERS-like Coronovirus" = "Bat MERS-like coronavirus", + "Monkey pox" = "Monkeypox virus", + "Morogoro virus" = "Morogoro mammarenavirus", + "SFVHpi" = "Simian foamy virus"))) + +## deal with taxonomy =========================================================== + +# Now: the taxonomy. First: generate a vector of every PREDICT_ virus name +predict_prefix <- predict %>% + dplyr::pull(VirusIntermediate) %>% + unique %>% stringr::str_subset("PREDICT_") %>% + stringr::str_split("-") %>% + unlist() %>% + stringr::str_subset("PREDICT_") %>% + unique() + +predict_tax <- data.frame(Virus = sort(predict_prefix), + full = NA, + VirusGenus = NA, + VirusFamily = NA, + VirusOrder = NA) + +predict_tax[1,2:5] <- c("Adeno-associated virus", "Dependoparvovirus", + "Parvoviridae", "Piccovirales") +predict_tax[2,2:5] <- c("Adenovirus", NA, "Adenoviridae", "Rowavirales") +predict_tax[3,2:5] <- c("Arenavirus", NA, "Arenaviridae", "Bunyavirales") +predict_tax[4,2:5] <- c("Bocaparvovirus", "Bocaparvovirus", "Parvoviridae", + "Picornavirales") +predict_tax[5,2:5] <- c("Coronavirus", NA, "Coronaviridae", "Nidovirales") +predict_tax[6,2:5] <- c("Enterovirus", "Enterovirus", "Picornaviridae", + "Picornavirales") +predict_tax[7,2:5] <- c("Flavivirus", NA, "Flaviviridae", "Amarillovirales") +predict_tax[8,2:5] <- c("Hantavirus", NA, "Hantaviridae", "Bunyavirales") +predict_tax[9,2:5] <- c("Herpesvirus", NA, "Herpesviridae", "Herpesvirales") +predict_tax[10,2:5] <- c("Lentivirus", "Lentivirus", "Retroviridae", + "Ortervirales") +predict_tax[11,2:5] <- c("Mamastrovirus", "Mamastrovirus", "Astroviridae", + "Stellavirales") +predict_tax[12,2:5] <- c("Murine norovirus", "Norovirus", "Caliciviridae", + "Picornavirales") +predict_tax[13,2:5] <- c("Orbivirus", "Orbivirus", "Reoviridae", "Reovirales") +predict_tax[14,2:5] <- c("Papillomavirus", NA, "Papillomaviridae", + "Zurhausenvirales") +predict_tax[15,2:5] <- c("Picobirnavirus", NA, "Picobirnaviridae", + "Durnavirales") +predict_tax[16,2:5] <- c("Phlebovirus", "Phleboviridae", "Phenuiviridae", + "Bunyavirales") +predict_tax[17,2:5] <- c("Picornavirus", NA, "Picornaviridae", + "Picornavirales") +predict_tax[18,2:5] <- c("Paramyxovirus", NA, "Paramyxoviridae", + "Mononegavirales") +predict_tax[19,2:5] <- c("Posavirus", NA, NA, "Picornavirales") +predict_tax[20,2:5] <- c("Poxvirus", NA, "Poxviridae", "Chitovirales") +predict_tax[21,2:5] <- c("Polyomavirus", NA, "Polyomaviridae", "Sepolyvirales") +predict_tax[22,2:5] <- c("Rhabdovirus", NA, "Rhabdoviridae", "Mononegavirales") +predict_tax[23,2:5] <- c("Seadornavirus", "Seadornavirus", + "Reoviridae", "Reovirales") + +predict_names <- predict %>% + dplyr::pull(VirusIntermediate) %>% + unique() + +predict_tax_big <- data.frame(FullName = + (predict_names %>% + stringr::str_subset("PREDICT_"))) + +predictionary <- predict_tax_big %>% + tidyr::separate( + col = FullName, + into = c("Virus","Number"), + sep = "-", + remove = FALSE) %>% + dplyr::left_join(predict_tax) %>% + dplyr::rename(Short = "Virus", Virus = "FullName") %>% + dplyr::select(-c("Short", "Number", "full")) + +# Check if literally any of these are NCBI resolved, which the vast majority are not + +# for (i in 1:nrow(predictionary)) { +# ncbi_num <- taxize::get_uid(predictionary$Virus[i]) +# ncbi_high <- taxize::classification(ncbi_num, db = "ncbi") +# if(!is_na(ncbi_high[[1]][1])){ +# predictionary$VirusNCBIResolved[i] <- TRUE +# predictionary$VirusTaxID[i] <- ncbi_num[[1]] +# } else { +# predictionary$VirusNCBIResolved[i] <- FALSE +# predictionary$VirusTaxID[i] <- NA +# } +# print(i) +# } + +predictionary$VirusNCBIResolved = FALSE +predictionary$VirusTaxID = NA +predictionary$VirusIntermediate = predictionary$Virus + +## test run of the NCBI part of this =========================================== + +ncbi_names <- predict %>% + dplyr::pull(VirusIntermediate) %>% + stringr::str_subset("PREDICT", negate = TRUE) %>% + unique() %>% + sort() + +# now using the self-made functions here +ncbi_tax <- vdict(ncbi_names) + +ncbi_tax %<>% dplyr::rename(VirusIntermediate = "VirusOriginal") + +# Add some guardrails ========================================================== +for (i in 1:nrow(ncbi_tax)) { + # "(?i)a" + # Only pull ones that haven"t already been queried + if(rlang::is_na(ncbi_tax$VirusOrder[i])){ + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)cytomegalovirus")) { + ncbi_tax$VirusGenus[i] <- "Cytomegalovirus" + ncbi_tax$VirusFamily[i] <- "Herpesviridae" + ncbi_tax$VirusOrder[i] <- "Herpesvirales" } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)adenovirus")) { + ncbi_tax$VirusFamily[i] <- "Adenoviridae" + ncbi_tax$VirusOrder[i] <- "Rowavirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)alphacoronavirus")) { + ncbi_tax$VirusGenus[i] <- "Alphacoronavirus" + ncbi_tax$VirusFamily[i] <- "Coronaviridae" + ncbi_tax$VirusOrder[i] <- "Nidovirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)betacoronavirus")) { + ncbi_tax$VirusGenus[i] <- "Betacoronavirus" + ncbi_tax$VirusFamily[i] <- "Coronaviridae" + ncbi_tax$VirusOrder[i] <- "Nidovirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)coronavirus")) { + ncbi_tax$VirusFamily[i] <- "Coronaviridae" + ncbi_tax$VirusOrder[i] <- "Nidovirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)paramyxovirus")) { + ncbi_tax$VirusFamily[i] <- "Paramyxoviridae" + ncbi_tax$VirusOrder[i] <- "Mononegavirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)foamy")) { + ncbi_tax$VirusGenus[i] <- "Spumavirus" + ncbi_tax$VirusFamily[i] <- "Retroviridae" + ncbi_tax$VirusOrder[i] <- "Ortervirales" + } + + #"Hantaviridae", "Bunyavirales") + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)hantavirus")) { + ncbi_tax$VirusFamily[i] <- "Hantaviridae" + ncbi_tax$VirusOrder[i] <- "Bunyavirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)bocavirus")) { + ncbi_tax$VirusGenus[i] <- "Bocaparvovirus" + ncbi_tax$VirusFamily[i] <- "Parvoviridae" + ncbi_tax$VirusOrder[i] <- "Picornavirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)lymphocryptovirus")) { + ncbi_tax$VirusGenus[i] <- "Lymphocryptovirus" + ncbi_tax$VirusFamily[i] <- "Herpesviridae" + ncbi_tax$VirusOrder[i] <- "Herpesvirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)herpesvirus")) { + ncbi_tax$VirusFamily[i] <- "Herpesviridae" + ncbi_tax$VirusOrder[i] <- "Herpesvirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)astrovirus")) { + ncbi_tax$VirusFamily[i] <- "Astroviridae" + ncbi_tax$VirusOrder[i] <- "Stellavirales" + } + + if(stringr::str_detect(ncbi_tax$Virus[i], "(?i)rhadinovirus")) { + ncbi_tax$VirusGenus[i] <- "Rhadinovirus" + ncbi_tax$VirusFamily[i] <- "Herpesviridae" + ncbi_tax$VirusOrder[i] <- "Herpesvirales" + } + } +} + +## manually deal with some naming ============================================== + +ncbi_tax[ncbi_tax$Virus=="YN12103/CHN/2012","VirusFamily"] <- + "Paramyxoviridae" +ncbi_tax[ncbi_tax$Virus=="YN12103/CHN/2012","VirusOrder"] <- + "Mononegavirales" + +ncbi_tax[ncbi_tax$Virus=="Trinidad/1FY2BA/2007","VirusGenus"] <- + "Alphacoronavirus" +ncbi_tax[ncbi_tax$Virus=="Trinidad/1FY2BA/2007","VirusFamily"] <- + "Coronaviridae" +ncbi_tax[ncbi_tax$Virus=="Trinidad/1FY2BA/2007","VirusOrder"] <- + "Nidovirales" + +ncbi_tax[ncbi_tax$Virus=="Philippines/Diliman1525G2/2008","VirusGenus"] <- + "Betacoronavirus" +ncbi_tax[ncbi_tax$Virus=="Philippines/Diliman1525G2/2008","VirusFamily"] <- + "Coronaviridae" +ncbi_tax[ncbi_tax$Virus=="Philippines/Diliman1525G2/2008","VirusOrder"] <- + "Nidovirales" + +# ### Merge + +predict %<>% dplyr::left_join(dplyr::bind_rows(predictionary, ncbi_tax)) + +# How many don"t have a genus? +predict %>% + dplyr::select(Virus, VirusGenus) %>% + unique() %>% + dplyr::filter(rlang::is_na(VirusGenus)) %>% + nrow() + +# merge up with the current NCBI species concepts where applicable ============= + +predict %<>% dplyr::ungroup() # Because of weird rowwise + +library(rentrez) +for(i in 1:nrow(predict)) { + if(predict$VirusNCBIResolved[i]=="FALSE" & !is.na(predict$Accession[i])){ + acc <- word(predict$Accession[i], 1, sep = ", ") + tax <- tryCatch(tax <- entrez_summary(db="nuccore", id = acc)$taxid, error = function(e) {NA}) + if(!is.na(tax)) { + ncbi.high <- taxize::classification(tax, db = "ncbi") + if(!is.na(ncbi.high[[1]][1])){ + if(!(any(str_detect(ncbi.high[[1]]$name[which(ncbi.high[[1]]$rank=='species')], c('unidentified', 'unclassified', 'sp.'))))) { + predict$VirusNCBIResolved[i] <- TRUE + if("species" %in% ncbi.high[[1]]$rank) {predict$Virus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='species'), 'name']} + if("genus" %in% ncbi.high[[1]]$rank) {predict$VirusGenus[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='genus'), 'name']} + if("family" %in% ncbi.high[[1]]$rank) {predict$VirusFamily[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='family'), 'name']} + if("order" %in% ncbi.high[[1]]$rank) {predict$VirusOrder[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='order'), 'name']} + if("class" %in% ncbi.high[[1]]$rank) {predict$VirusClass[i] <- ncbi.high[[1]][which(ncbi.high[[1]]$rank=='class'), 'name']} + + levels <- c("species", "genus", "family", "order", "class") + u <- last(ncbi.high[[1]][ncbi.high[[1]]$rank %in% levels,'id']) + predict$VirusTaxID[i] <- u + + print(ncbi.high) + } + } } } } -################################################################################################## -################################################################################################## -################################################################################################## -################################################################################################## -################################################################################################## -################################################################################################## -################################################################################################## -################################################################################################## -# Now, the host taxonomy -predict %<>% mutate(Host = recode(Host, !!!c("Hipposideros larvatus/grandis species complex" = "Hipposideros sp."))) -predict %>% pull(Host) %>% unique() -> hosts -host.tax <- hdict(hosts) -predict %>% rename(HostOriginal = "Host") %>% - left_join(host.tax) -> predict +for(i in 1:nrow(predict)) { + + if(predict$VirusNCBIResolved[i]=="FALSE" & + !rlang::is_na(predict$Accession[i])){ + + # accession value + acc <- stringr::word(predict$Accession[i], 1, sep = ", ") + + # try to get the taxonomic id + tax <- tryCatch(tax <- rentrez::entrez_summary( + db="nuccore", id = acc)$taxid, error = function(e) {NA}) + + # if it's not an NA, get a classification from NCBI + if(!is.na(tax)) { + + # get the ncbi + ncbi_high <- taxize::classification(tax, db = "ncbi") + + # if there are names continue + if(!is.na(ncbi_high[[1]][1])){ + + # check if the species names are unresolved + temp_name <- ncbi_high[[1]]$name[which(ncbi_high[[1]]$rank=="species")] + if(!(any(stringr::str_detect(temp_name, + c("unidentified", "unclassified", "sp."))))) { + + # this is putting in the resolved values + predict$VirusNCBIResolved[i] <- TRUE + if("species" %in% ncbi_high[[1]]$rank) {predict$Virus[i] <- + ncbi_high[[1]][which(ncbi_high[[1]]$rank=="species"), "name"]} + if("genus" %in% ncbi_high[[1]]$rank) {predict$VirusGenus[i] <- + ncbi_high[[1]][which(ncbi_high[[1]]$rank=="genus"), "name"]} + if("family" %in% ncbi_high[[1]]$rank) {predict$VirusFamily[i] <- + ncbi_high[[1]][which(ncbi_high[[1]]$rank=="family"), "name"]} + if("order" %in% ncbi_high[[1]]$rank) {predict$VirusOrder[i] <- + ncbi_high[[1]][which(ncbi_high[[1]]$rank=="order"), "name"]} + if("class" %in% ncbi_high[[1]]$rank) {predict$VirusClass[i] <- + ncbi_high[[1]][which(ncbi_high[[1]]$rank=="class"), "name"]} + + levels <- c("species", "genus", "family", "order", "class") + u <- dplyr::last(ncbi_high[[1]][ncbi_high[[1]]$rank %in% levels,"id"]) + predict$VirusTaxID[i] <- u + + print(ncbi_high) + } + } + } + } +} + +## host taxonomy =============================================================== + +predict %<>% dplyr::mutate( + Host = dplyr::recode( + Host, + !!!c("Hipposideros larvatus/grandis species complex" = "Hipposideros sp."))) + +hosts <- predict %>% + dplyr::pull(Host) %>% + unique() + +host_tax <- hdict(hosts) + +predict %<>% + dplyr::rename(HostOriginal = "Host") %>% + dplyr::left_join(host_tax) -predict %>% filter(is.na(Host)) %>% pull(HostOriginal) %>% unique() +# just a manual look +predict %>% filter(is_na(Host)) %>% pull(HostOriginal) %>% unique() predict %<>% select(-VirusIntermediate) -write_csv(predict, "Intermediate/Unformatted/PREDICTMainUnformatted.csv") +# write out intermediate ======================================================= +readr::write_csv( + predict, + here::here("Intermediate/Unformatted/PREDICTMainUnformatted.csv")) diff --git a/Code/02_3b_Digest GLOBI.R b/Code/02_3b_Digest GLOBI.R index 4b2539d..00bf20b 100644 --- a/Code/02_3b_Digest GLOBI.R +++ b/Code/02_3b_Digest GLOBI.R @@ -1,12 +1,12 @@ - -if(!exists('vdict')) {source('Code/001_TaxizeFunctions.R')} -if(!exists('jvdict')) {source('Code/001_Julia functions.R')} +source('Code/001_TaxizeFunctions.R') +source('Code/001_Julia functions.R') rentrez::set_entrez_key("ec345b39079e565bdfa744c3ef0d4b03ba08") library(tidyverse) library(taxize) library(magrittr) library(vroom) +install.ncbi() globi <- read_csv('Source/GLOBI-raw.csv') diff --git a/Code/Code_Dev/TaxonomyTempIn.csv b/Code/Code_Dev/TaxonomyTempIn.csv deleted file mode 100644 index 3de3487..0000000 --- a/Code/Code_Dev/TaxonomyTempIn.csv +++ /dev/null @@ -1,10883 +0,0 @@ -Name - -(Citrus unshiu x Citrus sinensis) x Citrus reticulata -[Brevibacterium] flavum -[Ruminococcus] gnavus ATCC 29149 -Abelmoschus -Abelmoschus angulosus -Abelmoschus caillei -Abelmoschus esculentus -Abelmoschus ficulneus -Abelmoschus manihot -Abelmoschus manihot subsp. tetraphyllus -Abelmoschus manihot var. tetraphyllus -Abelmoschus moschatus -Abelmoschus tuberculatus -Abeoforma whisleri -Abies lasiocarpa -Abramis brama -Abraxas grossulariatus -Abraxas tenuisuffusa -Abrosoma johorense -Abrothrix hirta -Abrothrix longipilis -Abrothrix olivaceus -Abrus precatorius -Abudefduf bengalensis -Abutilon -Abutilon glaucum -Abutilon indicum -Abutilon megapotamicum -Abutilon pannosum -Abutilon permolle -Abutilon theophrasti -Abutilon x hybridum -Acacia -Acalypha -Acalypha australis -Acalypha indica -Acanthamoeba -Acanthamoeba castellanii -Acanthamoeba castellanii str. Neff -Acanthamoeba polyphaga -Acanthamoeba sp. -Acanthaster planci -Acanthemblemaria sp. CUR14058.G -Acanthis flammea -Acanthocasuarina muellerianae -Acanthopagrus latus -Acanthopagrus schlegelii -Acanthophis antarcticus -Acanthorhynchus tenuirostris -Acanthosoma haemorrhoidale -Acanthospermum hispidum -Acanthurus bariene -Acanthurus dussumieri -Acanthurus triostegus -Acari -Acartia tonsa -Acaryochloris -Acaryochloris marina -Accipenser platorynchus -Accipiter -Accipiter cooperii -Accipiter fasciatus -Accipiter gentilis -Accipiter gentilis schvedowi -Accipiter gularis -Accipiter nisus -Accipiter striatus -Accipiter trivirgatus -Accipitridae -Accipitriformes -Acer pseudoplatanus -Acer pseudosieboldianum -Acerodon celebensis -Acetes -Acetes chinensis -Acetobacter -Acetobacter orleanensis -Acetobacter pasteurianus -Acetobacter sp. ATCC 21760 -Achaea faber -Achaea janata -Acheilognathus macropterus -Acheta domesticus -Achillea millefolium -Acholeplasma -Acholeplasma laidlawii -Achromobacter -Achromobacter animicus -Achromobacter denitrificans -Achromobacter marplatensis -Achromobacter sp. -Achromobacter xylosoxidans -Achyranthes aspera -Achyranthes bidentata -Achyranthes japonica -Acidianus -Acidianus brierleyi -Acidianus convivator -Acidianus hospitalis -Acidianus infernus -Acidianus pozzuoliensis -Acidianus sp. Acii26 -Acidianus uzoniensis -Acidithiobacillus caldus -Acidithiobacillus caldus ATCC 51756 -Acidovorax citrulli -Acinetobacter -Acinetobacter baumannii -Acinetobacter baumannii 1656-2 -Acinetobacter baumannii A118 -Acinetobacter baumannii AB5075 -Acinetobacter baumannii AB5256 -Acinetobacter baumannii ACICU -Acinetobacter baumannii ATCC 17978 -Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 -Acinetobacter baumannii MDR-TJ -Acinetobacter baumannii NIPH 201 -Acinetobacter baumannii NIPH 329 -Acinetobacter beijerinckii -Acinetobacter calcoaceticus -Acinetobacter genomosp. 16BJ -Acinetobacter halotolerans -Acinetobacter johnsonii -Acinetobacter nosocomialis -Acinetobacter nosocomialis M2 -Acinetobacter pittii -Acinetobacter radioresistens -Acinetobacter soli -Acinetobacter sp. -Acinonyx jubatus -Acinopterus angulatus -Acipenser baerii -Acipenser baerii baerii -Acipenser brevirostrum -Acipenser fulvescens -Acipenser gueldenstaedtii -Acipenser naccarii -Acipenser ruthenus -Acipenser stellatus -Acipenser transmontanus -Acmella oleracea -Acmella paniculata -Acomys cahirinus -Acomys dimidiatus -Acomys selousi -Acomys subspinosus -Acomys wilsoni -Aconitum -Aconitum carmichaelii -Aconitum fischeri -Acorus calamus -Acrantophis dumerili -Acremonium sclerotigenum -Acrida cinerea -Acridotheres -Acridotheres cristatellus -Acridotheres tristis -Acrocephalus dumetorum -Acrocephalus schoenobaenus -Acrocephalus scirpaceus -Acromyrmex -Acropoma japonicum -Acropora aspera -Acropora pruinosa -Actaea racemosa -Actias selene -Actinia equina -Actiniaria -Actinidia -Actinidia arguta -Actinidia chinensis -Actinidia deliciosa -Actinidia fortunatii -Actinidia glaucophylla -Actinidia guilinensis -Actinomyces -Actinomyces naeslundii -Actinomycetia bacterium -Actinomycetota -Actinoplanes -Actinoplanes sp. SN223/29 -Actitis macularius -activated sludge metagenome -Acyrthosiphon pisum -Addax -Adelphocoris fasciaticollis -Adenium obesum -Adenocalymma -Adiantum raddianum -Adonis ramosa -Adoxophyes honmai -Adoxophyes orana -Aechmophorus occidentalis -Aedeomyia catasticta -Aedeomyia madagascarica -Aedeomyia squamipennis -Aedes -Aedes abnormalis -Aedes aegypti -Aedes aegypti aegypti -Aedes africanus -Aedes alboannulatus -Aedes albolateralis -Aedes albopictus -Aedes alternans -Aedes bekkui -Aedes cinereus -Aedes circumluteolus -Aedes cumminsii -Aedes curtipes -Aedes dalzieli -Aedes dentatus -Aedes durbanensis -Aedes esoensis -Aedes flavopictus -Aedes furcifer -Aedes galloisi -Aedes gibbinsi -Aedes hensilli -Aedes japonicus -Aedes japonicus japonicus -Aedes koreicus -Aedes lineatopennis -Aedes luteocephalus -Aedes mcintoshi -Aedes metallicus -Aedes nipponicus -Aedes niveus -Aedes notoscriptus -Aedes ochraceus -Aedes opok -Aedes palpalae -Aedes pembaensis -Aedes rossicus -Aedes simpsoni -Aedes sp. -Aedes taylori -Aedes togoi -Aedes tremulus -Aedes tricholabis -Aedes vexans -Aedes vexans nipponii -Aedes vittatus -Aegilops kotschyi -Aegithalos caudatus -Aegle marmelos -Aegopodium podagraria -Aegypius monachus -Aeonium -Aeorestes cinereus -Aepyceros -Aepyceros melampus -Aeribacillus pallidus -Aeridinae -Aerococcus viridans -Aeromonas -Aeromonas caviae -Aeromonas dhakensis -Aeromonas hydrophila -Aeromonas media -Aeromonas popoffii -Aeromonas rivipollensis -Aeromonas salmonicida -Aeromonas salmonicida subsp. salmonicida -Aeromonas schubertii -Aeromonas sp. -Aeromonas sp. ARM81 -Aeromonas sp. IS4 -Aeromonas sp. MR16 -Aeromonas sp. MR19 -Aeromonas sp. MR7 -Aeromonas veronii -Aeromonas veronii bv. sobria -Aeropyrum pernix -Aeropyrum pernix K1 -Aeschynomene virginica -Aesopia cornuta -Aethina tumida -Aethomys chrysophilus -Aethomys hindei medicatus -Aethomys ineptus -Aethomys kaiseri -Afronycteris nana -Agama agama -Agamia agami -Agapanthus -Agapanthus africanus -Agapanthus praecox -Agapornis -Agapornis fischeri -Agapornis nigrigenis -Agapornis personatus -Agapornis pullarius -Agapornis roseicollis -Agapornis swindernianus -Agaricus bisporus -Agastache rugosa -Agathobaculum butyriciproducens -Agave -Agave amica -Agave attenuata -Agave fourcroydes -Agave sisalana -Agave tequilana -Agelaius phoeniceus -Agelena labyrinthica -Ageratina adenophora -Ageratina altissima -Ageratum -Ageratum conyzoides -Ageratum houstonianum -Aggregatibacter actinomycetemcomitans -Aggregatibacter actinomycetemcomitans D11S-1 -Aglaonema modestum -Agraulis -Agrimonia -Agrimonia pilosa -Agrobacterium -Agrobacterium fabacearum -Agrobacterium tumefaciens -Agropsar sturninus -Agrostis magellanica -Agrostis stolonifera -Agrotis exclamationis -Agrotis ipsilon -Agrotis segetum -Ailanthus -Ailanthus altissimus -Ailuropoda -Ailuropoda melanoleuca -Ailurus fulgens -Aiptasia -Aix galericulata -Aix sponsa -Ajuga reptans -Akkermansia muciniphila -Akodon -Akodon azarae -Akodon cursor -Akodon montensis -Akodon paranaensis -Akodon serrensis -Akodon simulator -Alauda arvensis -Albatrellopsis flettii -Albizia chinensis -Albizia lebbeck -Albuca -Albula vulpes -Alcaligenes faecalis -Alcea -Alcea rosea -Alcea striata -Alcedinidae -Alcelaphus -Alcelaphus buselaphus -Alces alces -Alces americanus -Alectoris barbara -Alectoris chukar -Alectoris graeca -Alectoris rufa -Alectorobius amblus -Alectorobius capensis -Alectorobius coniceps -Alectorobius denmarki -Alectorobius maritimus -Alectorobius muesebecki -Alectorobius tadaridae -Alexandromys oeconomus -Aleyrodidae -Alhagi sparsifolia -Alicyclobacillus acidoterrestris -Aliivibrio fischeri -Aliivibrio fischeri ES114 -Alishewanella sp. SMS8 -Alisterus amboinensis -Alisterus scapularis -Alistipes shahii -Alistipes sp. -Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1.3604 -Alkalihalobacillus bogoriensis -Alkalihalobacillus pseudalcaliphilus -Alkalihalophilus pseudofirmus -Alkalimonas collagenimarina -Alkekengi officinarum -Allamanda cathartica -Allenopithecus nigroviridis -Alliaria petiolata -Allium -Allium ampeloprasum -Allium angulosum -Allium ascalonicum -Allium caeruleum -Allium cepa -Allium cepa var. aggregatum -Allium chinense -Allium fistulosum -Allium giganteum -Allium karataviense -Allium loratum -Allium macrostemon -Allium neapolitanum -Allium oschaninii -Allium sativum -Allium scorodoprasum -Allium stracheyi -Allium subhirsutum -Allium tuberosum -Allium vineale -Allium x proliferum -Allochrocebus lhoesti -Allochrocebus preussi -Allochrocebus solatus -Allocricetulus eversmanni -Allonemobius socius -Alloteropsis angusta -Alloteropsis semialata -Alocasia -Aloha -Alopecurus myosuroides -Alopecurus pratensis -Alopochen aegyptiaca -Alosa pseudoharengus -Alouatta -Alouatta belzebul -Alouatta caraya -Alouatta guariba -Alouatta guariba clamitans -Alouatta macconnelli -Alouatta palliata -Alouatta pigra -Alouatta sara -Alouatta seniculus -Alouatta sp. -Alphaproteobacteria -Alpheus distinguendus -Alphitobius diaperinus -Alpinia galanga -Alpinia oxyphylla -Alpinia purpurata -Alstroemeria -Alstroemeria pulchella -Alstroemeria sp. -Alternanthera -Alternanthera ficoidea -Alternanthera philoxeroides -Alternanthera pungens -Alternanthera sessilis -Alternaria alternata -Alternaria arborescens -Alternaria brassicicola -Alternaria cerealis -Alternaria dianthicola -Alternaria longipes -Alternaria solani -Alternaria tenuissima -Alternaria triticina -Alteromonadaceae -Alteromonas -Alteromonas abrolhosensis -Alteromonas confluentis -Alteromonas gracilis -Alteromonas litorea -Alteromonas macleodii -Alteromonas macleodii ATCC 27126 -Alteromonas macleodii str. 'Balearic Sea AD45' -Alteromonas marina -Alteromonas mediterranea -Alteromonas sp. -Althaea -Althaea officinalis -Altica cyanea -Altolamprologus compressiceps -Alveonasus lahorensis -Alytes obstetricans -Amandava amandava -Amaranthus -Amaranthus blitum -Amaranthus caudatus -Amaranthus cruentus -Amaranthus deflexus -Amaranthus dubius -Amaranthus graecizans -Amaranthus hybridus -Amaranthus hypochondriacus -Amaranthus palmeri -Amaranthus retroflexus -Amaranthus spinosus -Amaranthus thunbergii -Amaranthus tricolor -Amaranthus tuberculatus -Amaranthus viridis -Amaryllis -Amaryllis belladonna -Amata phegea -Amaurornis phoenicurus -Amazona aestiva -Amazona albifrons -Amazona amazonica -Amazona arausiaca -Amazona auropalliata -Amazona autumnalis -Amazona barbadensis -Amazona brasiliensis -Amazona farinosa -Amazona festiva -Amazona leucocephala -Amazona ochrocephala -Amazona ochrocephala auropalliata -Amazona ochrocephala panamensis -Amazona oratrix -Amazona rhodocorytha -Amazona sp. -Amazona ventralis -Amazona vinacea -Amazona viridigenalis -Amazona xantholora -Ambassis marianus -Ambispora leptoticha -Ambloplites rupestris -Amblychaeturichthys hexanema -Amblygaster clupeoides -Amblygaster leiogaster -Amblyomma -Amblyomma americanum -Amblyomma cajennense -Amblyomma dissimile -Amblyomma gemma -Amblyomma geoemydae -Amblyomma javanense -Amblyomma lepidum -Amblyomma longirostre -Amblyomma moreliae -Amblyomma nuttalli -Amblyomma ovale -Amblyomma sculptum -Amblyomma sp. -Amblyomma sparsum -Amblyomma testudinarium -Amblyomma varanense -Amblyomma variegatum -Ambrosia artemisiifolia -Ambrosia psilostachya -Ambrosia trifida -Ambrosiozyma kashinagicola -Ambystoma maculatum -Ambystoma mavortium -Ambystoma mexicanum -Ambystoma opacum -Ambystoma tigrinum -Amedibacillus -Ameiurus melas -Ameiurus nebulosus -Ameiva ameiva -Amelanchier -Amelanchier alnifolia -Amelanchier arborea -Amelanchier ovalis -Aminobacter sp. MSH1 -Amitermes -Ammi majus -Ammodytes personatus -Ammophila sabulosa -Ammotragus lervia -Amoeba -Amoeba sp. -Amolops mantzorum -Amomum subulatum -Amorbia cuneana -Amorbia synneurana -Amorphophallus -Amorphophallus konjac -Amorphophallus paeoniifolius -Amorphophallus paeoniifolius var. campanulatus -Ampelopsis cordata -Amphibalanus rhizophorae -Amphibia -Amphibola crenata -Amphiprion clarkii -Amphiprion ocellaris -Amphiprion percula -Amphiprion sebae -Amphiprora -Amphipsocus japonicus -Amrasca biguttula -Amsacta albistriga -Anabaena -Anabarhynchus dentiphallus -Anabas testudineus -Anacamptis morio -Anadenanthera colubrina -Anaerostipes caccae -Anagallis arvensis -Anagrapha falcifera -Anagyrus vladimiri -Ananas comosus -Ananas comosus var. erectifolius -Ananas comosus var. parguazensis -Anarhichas lupus -Anarta trifolii -Anartia jatrophae -Anas -Anas acuta -Anas bahamensis -Anas capensis -Anas carolinensis -Anas castanea -Anas crecca -Anas cyanoptera -Anas diazi -Anas erythrorhyncha -Anas flavirostris -Anas fulvigula -Anas georgica -Anas gracilis -Anas melleri -Anas platyrhynchos -Anas platyrhynchos platyrhynchos -Anas poecilorhyncha -Anas puna -Anas rubripes -Anas sp. -Anas superciliosa -Anas undulata -Anas versicolor -Anas zonorhyncha -Anastomus oscitans -Anatidae -Anatidae sp. -Anatinae -Anax junius -Anaxyrus boreas boreas -Anchusa -Anchusa officinalis -Anchusa undulata -Ancistrocerus auctus -Ancistrocerus nigricornis -Andraca bipunctata -Andrena -Andrena (Melandrena) sp. EM-2018 -Andrena cineraria -Andrena distinguenda -Andrena ferrugineicrus -Andrena flavipes -Andrena fulva -Andrena haemorrhoa -Andrena hattorfiana -Andrena humilis -Andrena impunctata -Andrena lagopus -Andrena nitida -Andrena sp. -Andrena vaga -Andrena ventricosa -Andrias davidianus -Andricus hakonensis -Andrographis paniculata -Androlaelaps casalis -Andropogon gerardi -Andropogon virginicus -Anelosimus studiosus -Anemone -Anemone blanda -Anemone coronaria -Anemone flaccida -Anemone x hybrida -Anethum -Anethum foeniculum -Anethum graveolens -Angelica dahurica -Angelica genuflexa -Angelica gigas -Angelica keiskei -Angelica lucida -Angelica sinensis -Angelonia -Angelonia angustifolia -Anguilla -Anguilla anguilla -Anguilla australis -Anguilla dieffenbachii -Anguilla japonica -Anguilla marmorata -Anguilla rostrata -Anguillidae -Anguilliformes -Anhinga -Anisodontea -Anisomeles indica -Anisopteromalus calandrae -Annelida -Annona squamosa -Anoda cristata -Anodorhynchus hyacinthinus -Anodorhynchus leari -Anolis allogus -Anolis carolinensis -Anolis distichus ignigularis -Anolis distichus ravitergum -Anolis sagrei -Anomala cuprea -Anomis sabulifera -Anopheles -Anopheles albimanus -Anopheles albitarsis -Anopheles algeriensis -Anopheles amictus -Anopheles annularis -Anopheles annulipes -Anopheles atroparvus -Anopheles atropos -Anopheles bancroftii -Anopheles barbirostris -Anopheles boliviensis -Anopheles claviger -Anopheles coluzzii -Anopheles coustani -Anopheles crucians -Anopheles cruzii -Anopheles darlingi -Anopheles epiroticus -Anopheles farauti -Anopheles freeborni -Anopheles funestus -Anopheles gambiae -Anopheles hinesorum -Anopheles hyrcanus -Anopheles maculatus -Anopheles maculipennis -Anopheles meraukensis -Anopheles messeae -Anopheles minimus -Anopheles nimbus -Anopheles nuneztovari -Anopheles pauliani -Anopheles pharoensis -Anopheles plumbeus -Anopheles pretoriensis -Anopheles pseudopictus -Anopheles pseudopunctipennis -Anopheles pseudowillmori -Anopheles punctipennis -Anopheles quadrimaculatus -Anopheles sacharovi -Anopheles sinensis -Anopheles sp. -Anopheles squamosus -Anopheles stephensi -Anopheles subpictus -Anopheles superpictus -Anopheles tenebrosus -Anopheles tessellatus -Anopheles triannulatus -Anopheles vagus -Anopheles yatsushiroensis -Anopheles ziemanni -Anoplolepis gracilipes -Anoplotrupes stercorosus -Anoura caudifer -Anoura geoffroyi -Anourosorex squamipes -Anourosorex yamashinai -Anous minutus -Anous stolidus -Anous tenuirostris -Anoxybacillus caldiproteolyticus -Anredera cordifolia -Anser -Anser albifrons -Anser anser -Anser anser domesticus -Anser brachyrhynchus -Anser caerulescens -Anser caerulescens atlantica -Anser caerulescens caerulescens -Anser canagicus -Anser cygnoides -Anser cygnoides domesticus -Anser erythropus -Anser fabalis -Anser indicus -Anser rossii -Anser sp. -Anseriformes -Antaresia maculosa -Antaresia perthensis -Antaresia stimsoni -Antechinus -Antennarius striatus -Anthemis arvensis -Antheraea assamensis -Antheraea mylitta -Antheraea pernyi -Antheraea pernyi x Antherea roylei -Antheraea polyphemus -Antheraea yamamai -Anthidium florentinum -Anthidium loti -Anthidium manicatum -Anthocercis gracilis -Anthocercis ilicifolia -Anthocercis littorea -Anthocercis viscosa -Anthochaera chrysoptera -Anthophila fabriciana -Anthophora plumipes -Anthornis melanura -Anthoxanthum odoratum -Anthoxanthum redolens -Anthriscus cerefolium -Anthriscus sylvestris -Anthurium -Anthurium amnicola -Anthurium andraeanum -Anthus berthelotii -Anthus rufulus -Anticarsia gemmatalis -Antidorcas marsupialis -Antigone canadensis -Antigone canadensis pulla -Antigone vipio -Antilocapra americana -Antilope cervicapra -Antipaluria urichi -Antirrhinum majus -Antirrhinum sp. -Antonospora locustae -Antricola delacruzi -Antrostomus carolinensis -Antrozous pallidus -Anura -Anurida maritima -Aonyx cinereus -Aotus azarai -Aotus griseimembra -Aotus nancymaae -Aotus trivirgatus -Aotus vociferans -Apalone -Apalone ferox -Apanteles sp. -Apera spica-venti -Apertochrysa flavifrons flavifrons -Apertochrysa ventralis -Aphalara polygoni -Aphanizomenon flos-aquae -Aphanochaete repens -Aphelinus abdominalis -Aphelocoma -Aphelocoma californica -Aphididae -Aphis -Aphis citricidus -Aphis craccivora -Aphis fabae -Aphis glycines -Aphis gossypii -Aphis idaei -Aphis nerii -Aphrophora alni -Apidae -Apidae sp. -Apinae -Apios americana -Apis -Apis andreniformis -Apis cerana -Apis cerana cerana -Apis cerana indica -Apis cerana japonica -Apis dorsata -Apis florea -Apis mellifera -Apis mellifera adansonii -Apis mellifera carnica -Apis mellifera carpatica -Apis mellifera intermissa -Apis mellifera ligustica -Apis mellifera scutellata -Apium graveolens -Apium graveolens Dulce Group -Apium graveolens Secalinum Group -Apium prostratum -Aplodinotus grunniens -Aplosporella javeedii -Aplysina aerophoba -Apocheima cinerarius -Apocrita -Apocryptophagus -Apocynaceae -Apodemus -Apodemus agrarius -Apodemus agrarius ningpoensis -Apodemus argenteus -Apodemus chejuensis -Apodemus chevrieri -Apodemus draco -Apodemus flavicollis -Apodemus ilex -Apodemus latronum -Apodemus peninsulae -Apodemus ponticus -Apodemus speciosus -Apodemus sylvaticus -Apodemus uralensis -Apodinae -Apophua simplicipes -Aporia crataegi -Apostichopus californicus -Aprosmictus erythropterus -Aptenodytes patagonicus -Apteryx rowi -Apus apus -Aquamicrobium -Aquamicrobium sp. H14 -Aquificae -Aquila adalberti -Aquila audax -Aquila chrysaetos -Aquila fasciata -Aquila heliaca -Aquilegia buergeriana -Aquilegia canadensis -Aquilegia japonica -Aquilegia sp. -Aquilegia viridiflora -Ara -Ara ambiguus -Ara ararauna -Ara chloropterus -Ara glaucogularis -Ara macao -Ara militaris -Ara rubrogenys -Ara severus -Arabidopsis -Arabidopsis halleri -Arabidopsis halleri subsp. gemmifera -Arabidopsis thaliana -Araceae -Arachis -Arachis glabrata -Arachis hypogaea -Arachis pintoi -Arachis repens -Arachis villosulicarpa -Arachnis labrosa -Aralia elata -Araneae -Araneae sp. -Aratinga -Aratinga auricapillus -Aratinga jandaya -Aratinga nenday -Aratinga solstitialis -Aratinga sp. -Aratus pisonii -Araujia sericifera -Arceuthobium sichuanense -Archaea -Archaeolacerta bedriagae -Arctium lappa -Arctium tomentosum -Arctocephalus -Arctocephalus australis -Arctocephalus forsteri -Arctocephalus gazella -Arctocephalus tropicalis -Arctopus echinatus -Arctotheca calendula -Arctotis -Ardea alba -Ardea cinerea -Ardea herodias -Ardea purpurea -Ardeidae -Ardenna carneipes -Ardenna pacifica -Ardeola -Ardeola bacchus -Ardeola grayii -Areca catechu -Arecaceae -Arenaria interpres -Argas -Argas abdussalami -Argas arboreus -Argas cooleyi -Argas hermanni -Argas japonicus -Argas miniatus -Argas persicus -Argas reflexus -Argas robertsi -Argas sp. -Argas vulgaris -Argentina silus -Argentina sphyraena -Argiope bruennichi -Argopecten irradians -Argyranthemum frutescens -Argyrochosma nivea -Argyrosomus regius -Ariadne merione -Arisaema -Arisaema heterophyllum -Aristolochia -Aristolochia arcuata -Aristolochia fimbriata -Aristolochia gibertii -Aristolochia zollingeriana -Aristotelia chilensis -Arma chinensis -Armadillidium decorum -Armadillidium vulgare -Armigeres -Armigeres durhami -Armigeres obturbans -Armigeres subalbatus -Armillaria borealis -Armillaria cepistipes -Armillaria luteobubalina -Armillaria mellea -Armillaria novae-zelandiae -Armillaria ostoyae -Armillaria sp. -Armoracia rusticana -Arnoglossus -Aroa discalis -Aronia melanocarpa -Arracacia -Arracacia xanthorrhiza -Arremon taciturnus -Arrhenatherum elatius -Arripis georgianus -Arsenophonus nasoniae -Arsenophonus sp. -Artaxa digramma -Artemia sinica -Artemia sp. -Artemisia annua -Artemisia capillaris -Artemisia carvifolia -Artemisia princeps -Artemisia verlotiorum -Artemisina melana -Arthrobacter -Arthrobacter globiformis -Arthrobacter sp. -Arthrobacter sp. 68b -Arthrobacter sp. ATCC 21022 -Arthrocladiella mougeotii -Arthronema africanum -Arthropoda -Arthropodium cirratum -Artibeus -Artibeus cinereus -Artibeus fimbriatus -Artibeus glaucus watsoni -Artibeus jamaicensis -Artibeus lituratus -Artibeus obscurus -Artibeus phaeotis -Artibeus planirostris -Artocarpus altilis -Arundina graminifolia -Arundinax aedon -Arvicanthis niloticus -Arvicanthis sp. -Arvicola amphibius -Ascaris suum -Asclepias curassavica -Asclepias syriaca -Asclepias viridis -Ascosphaera apis -Aselliscus stoliczkanus -Asellus -Asgard group archaeon -Asimina triloba -Asio flammeus -Asio otus -Asparagus -Asparagus declinatus -Asparagus officinalis -Asparagus rubicundus -Aspergillus creber -Aspergillus ellipticus -Aspergillus flavus -Aspergillus foetidus -Aspergillus fumigatus -Aspergillus heteromorphus -Aspergillus homomorphus -Aspergillus lentulus -Aspergillus neoniger -Aspergillus nidulans -Aspergillus niger -Aspergillus ochraceoroseus -Aspergillus ochraceus -Aspergillus protuberus -Aspergillus pseudoglaucus -Aspergillus pseudoviridinutans -Aspergillus spelaeus -Aspergillus tennesseensis -Aspergillus terreus -Aspergillus thermomutatus -Aspergillus tubingensis -Aspidistra elatior -Aspidites melanocephalus -Aspidites ramsayi -Aspidoptera -Asplenium nidus -Astacoidea -Aster -Aster alpinus -Aster indicus -Aster scaber -Asteraceae -Asterias forbesi -Asterias rubens -Asteriscus aquaticus -Asteroidea -Asterropteryx semipunctata -Asterropteryx spinosa -Astilbe x arendsii -Astragalus -Astragalus myriacanthus -Astragalus sinicus -Astronium fraxinifolium -Astronotus ocellatus -Astropecten polyacanthus -Astrosyne radiata -Astyanax mexicanus -Asystasia -Asystasia gangetica -Atelerix albiventris -Ateles belzebuth -Ateles chamek -Ateles fusciceps -Ateles geoffroyi -Ateles hybridus -Ateles paniscus -Ateles sp. -Atelura formicaria -Athelia rolfsii -Athene noctua -Atherigona orientalis -Atheris -Atheris squamigera -Atilax paludinosus -Atomaria fuscata -Atractomorpha sinensis -Atractomorpha sp. (in: grasshoppers) -Atractylodes lancea -Atractylodes macrocephala -Atrina pectinata -Atriplex -Atriplex micrantha -Atriplex semilunaris -Atropa belladonna -Atropus armatus -Atta cephalotes -Atyidae -Aubrieta -Aucuba japonica -Aucuba japonica var. variegata -Augochlora pura -Augusta -Aulacomnium heterostichum -Aulacophora lewisii -Aulacorthum magnoliae -Aulonocranus dewindti -Aurantimonas sp. C5-1 -Aureococcus anophagefferens -Auricularia heimuer -Austroagallia caboverdensis -Austroargiolestes icteromelas -Austrophasmatidae -Austropotamobius pallipes -Austrosimulium australense -Austrovenus stutchburyi -Autographa californica -Autographa gamma -Autographa nigrisigna -Automeris liberia -Avena byzantina -Avena fatua -Avena sativa -Avena sp. -Avena sterilis -Avena strigosa -Averrhoa carambola -Aves -Aves sp. -Axis axis -Axis porcinus -Axonopus compressus -Aythya -Aythya affinis -Aythya americana -Aythya baeri -Aythya collaris -Aythya ferina -Aythya fuligula -Aythya marila -Aythya nyroca -Aythya valisineria -Azadirachta indica -Azolla filiculoides -Azorella polaris -Azorina vidalii -Azospirillum brasilense -Babyrousa babyrussa -Bacillota -Bacillus -Bacillus amyloliquefaciens -Bacillus anthracis -Bacillus anthracis str. Sterne -Bacillus australimaris -Bacillus cereus -Bacillus cereus ATCC 14579 -Bacillus cereus ATCC 4342 -Bacillus cereus BGSC 6E1 -Bacillus cereus BtB2-4 -Bacillus cereus IS075 -Bacillus cereus NC7401 -Bacillus cereus VD166 -Bacillus cereus VD184 -Bacillus mycoides -Bacillus pumilus -Bacillus pumilus BL8 -Bacillus pumilus SAFR-032 -Bacillus safensis -Bacillus sp. (in: firmicutes) -Bacillus sp. 6k512 -Bacillus sp. ET1 -Bacillus subtilis -Bacillus subtilis BEST7003 -Bacillus subtilis subsp. natto -Bacillus subtilis subsp. subtilis str. 168 -Bacillus tequilensis -Bacillus thuringiensis -Bacillus thuringiensis serovar israelensis -Bacillus thuringiensis serovar kurstaki -Bacillus thuringiensis serovar tenebrionis -Bacillus thuringiensis serovar tenebrionis str. YBT-1765 -Bacillus thuringiensis YBT-1518 -Bacillus velezensis FZB42 -Bacopa -Bacopa monnieri -Bacteria -Bactericera cockerelli -Bactericera trigonica -bacterium -Bacteroides -Bacteroides caccae -Bacteroides cellulosilyticus -Bacteroides fragilis -Bacteroides intestinalis -Bacteroides ovatus -Bacteroides salyersiae -Bacteroides sp. -Bacteroides thetaiotaomicron -Bacteroides thetaiotaomicron VPI-5482 -Bacteroides uniformis -Bacteroides xylanisolvens -Bactrocera correcta -Bactrocera dorsalis -Bactrocera frauenfeldi -Bactrocera kraussi -Bactrocera latifrons -Bactrocera minax -Bactrocera musae -Bactrocera oleae -Bactrocera tryoni -Bactrocera zonata -Baeolophus bicolor -Baeolophus inornatus -Baiomys musculus -Baiomys taylori -Balaena mysticetus -Balaenoptera acutorostrata -Balaenoptera physalus -Balearica pavonina -Balearica regulorum -Balionycteris maculata -Baliospermum solanifolium -Balistapus -Balta vilis -Bambusa -Bambusa albolineata -Bambusa beecheyana -Bambusa bicicatricata -Bambusa boniopsis -Bambusa cerosissima -Bambusa chungii -Bambusa contracta -Bambusa cornigera -Bambusa distegia -Bambusa emeiensis -Bambusa eutuldoides -Bambusa flexuosa -Bambusa funghomii -Bambusa gibba -Bambusa lenta -Bambusa longispiculata -Bambusa multiplex -Bambusa multiplex var. multiplex -Bambusa oldhamii -Bambusa pachinensis -Bambusa pervariabilis -Bambusa prominens -Bambusa remotiflora -Bambusa rigida -Bambusa rutila -Bambusa surrecta -Bambusa textilis -Bambusa ventricosa -Bambusa vulgaris -Bambusa xiashanensis -Bambuseae -Bambusoideae -Bandicota bengalensis -Bandicota indica -Bandicota savilei -Bandicota sp. -Banjos banjos -Barbastella barbastellus -Barbus barbus -Barkeria -Barleria cristata -Barleria repens -Barnardius zonarius -Barnardius zonarius semitorquatus -Bartonella henselae -Bartonella quintana -Bartonella vinsonii -Basella alba -Basidentitermes aurivillii -Basileuterus culicivorus -Bassariscus astutus -Bathilda ruficauda -Bathybates fasciatus -Bathycoccus -Bathycoccus prasinos -Bathyergus suillus -Batillaria zonalis -Batis maritima -Bauhinia variegata -Bdellocephala annandalei -Bdelloura candida -Bdellovibrio -Bdellovibrio bacteriovorus -Beauveria bassiana -Begonia -Begonia bowerae -Begonia cucullata -Begonia grandis -Begonia odorata -Begonia x hiemalis -Begonia x semperflorens-cultorum -Begonia x tuberhybrida -Bellamya -Belone belone -Belostoma flumineum -Bemisia tabaci -Benincasa fistulosa -Benincasa hispida -Benthochromis horii -Berberis -Berkeleyomyces basicola -Beroe forskalii -Berylmys bowersi -Beta -Beta vulgaris -Beta vulgaris subsp. maritima -Beta vulgaris subsp. vulgaris -Betta splendens -Bettongia penicillata -Betula -Betula nigra -Betula pendula -Betula pubescens -Betula pubescens var. pumila -Betula sp. -Bibio marci -Bidens -Bidens alba -Bidens frondosa -Bidens pilosa -Bidens tripartita -Bifidobacterium adolescentis -Bifidobacterium asteroides -Bifidobacterium bifidum -Bifidobacterium dentium -Bifidobacterium pseudocatenulatum -Bifidobacterium thermophilum -Bignonia -Biomphalaria glabrata -Biomphalaria pfeifferi -Bipolaris maydis -Bipolaris oryzae -Bison -Bison bison -Bison bonasus -Biston robustus -Biston suppressaria -Bitis atropos -Bitis gabonica -Bitis nasicornis -Bituminaria bituminosa -Bivalvia -Blainvillea rhomboidea -Blanus cinereus -Blarina brevicauda -Blarina carolinensis -Blarina hylophaga -Blastocerus dichotomus -Blastocystis hominis -Blattella -Blattella germanica -Blattodea -Blechomonas juanalfonzi -Blechomonas luni -Blechomonas maslovi -Blechomonas wendygibsoni -Blenniella -Blephilia hirsuta -Bletilla striata -Blicca bjoerkna -Boa -Boa constrictor -Boa imperator -Boana pugnax -Bobilla -Bodo saltans -Boehmeria -Boehmeria leiophylla -Boehmeria nivea -Boerhavia -Boerhavia coccinea -Boerhavia diffusa -Boerhavia erecta -Boiga irregularis -Bolbocoleon piliferum -Bolborhynchus lineola -Bolbostemma paniculatum -Boleophthalmus pectinirostris -Bombus -Bombus campestris -Bombus cryptarum -Bombus hortorum -Bombus humilis -Bombus hypnorum -Bombus ignitus -Bombus impatiens -Bombus lantschouensis -Bombus lapidarius -Bombus lucorum -Bombus pascuorum -Bombus patagiatus -Bombus pratorum -Bombus ruderarius -Bombus ruderatus -Bombus rupestris -Bombus sitkensis -Bombus sp. -Bombus sylvarum -Bombus sylvestris -Bombus ternarius -Bombus terrestris -Bombus vagans -Bombus vestalis -Bombycilla cedrorum -Bombycilla garrulus -Bombylius sp. -Bombyx mandarina -Bombyx mori -Bonasa umbellus -Bondarzewia berkeleyi -Boophilus -Boops boops -Borago officinalis -Bordetella -Bordetella avium -Bordetella bronchiseptica -Bos -Bos frontalis -Bos gaurus -Bos grunniens -Bos indicus -Bos indicus x Bos taurus -Bos javanicus -Bos mutus -Bos primigenius -Bos sp. -Bos taurus -Boselaphus tragocamelus -Botaurus stellaris -Bothriocroton hydrosauri -Botrylloides leachii -Botryosphaeria dothidea -Botrytis -Botrytis cinerea -Botrytis porri -Bougainvillea -Bougainvillea glabra -Bougainvillea peruviana -Bougainvillea spectabilis -Boulengerochromis microlepis -Bouvardia -Bovidae -Bracharoa mixta -Brachiaria -Brachiaria umbellata -Brachiomonas submarina -Brachionus plicatilis -Brachygaster minutus -Brachymystax lenok -Brachypodium distachyon -Brachypodium retusum -Brachyspira hyodysenteriae -Brachyteles arachnoides -Bradybaena similaris -Bradypus tridactylus -Bradypus variegatus -Bradyrhizobium diazoefficiens -Bradyrhizobium elkanii USDA 76 -Bradyrhizobium japonicum -Branchiopoda -Branchiostoma belcheri -Branta bernicla -Branta canadensis -Branta hutchinsii -Branta leucopsis -Branta ruficollis -Branta sandvicensis -Brassica -Brassica carinata -Brassica cretica -Brassica juncea -Brassica juncea subsp. napiformis -Brassica napus -Brassica napus subsp. rapifera -Brassica napus var. napus -Brassica nigra -Brassica oleracea -Brassica oleracea var. botrytis -Brassica oleracea var. capitata -Brassica oleracea var. gemmifera -Brassica oleracea var. gongylodes -Brassica oleracea var. italica -Brassica oleracea var. oleracea -Brassica oleracea var. sabellica -Brassica oleracea var. viridis -Brassica rapa -Brassica rapa Broccoletto Group -Brassica rapa subsp. chinensis -Brassica rapa subsp. oleifera -Brassica rapa subsp. pekinensis -Brassica rapa subsp. rapa -Brassica rapa var. parachinensis -Brassica rapa var. perviridis -Brassica rapa var. rapa -Brassica sp. -Brassicaceae -Braula coeca -Bremia lactucae -Brevibacillus laterosporus -Brevibacterium aurantiacum -Brevibacterium fuscum -Brevibacterium iodinum -Brevicoryne brassicae -Brevundimonas -Brevundimonas goettingensis -Brevundimonas pondensis -Brevundimonas subvibrioides ATCC 15264 -Breynia androgyna -Broadleysaurus major -Brochothrix thermosphacta -Bromelia laciniosa -Bromelia pinguin -Bromus -Bromus catharticus -Bromus commutatus -Bromus diandrus -Bromus hordeaceus -Bromus scoparius -Bromus secalinus -Bromus sterilis -Bromus tomentellus -Brontispa longissima -Brotogeris tirica -Broussonetia kazinoki -Broussonetia papyrifera -Browallia americana -Brucella abortus -Brucella abortus 544 -Brucella abortus S19 -Brucella anthropi -Brucella canis -Brucella inopinata -Brucella intermedia -Brucella melitensis -Brucella melitensis bv. 1 str. 16M -Brucella sp. -Brugmansia -Brugmansia arborea -Brugmansia aurea -Brugmansia sanguinea -Brugmansia suaveolens -Brugmansia versicolor -Brugmansia x candida -Bryonia dioica -Bryopsis cinicola -Bubalus -Bubalus bubalis -Bubalus carabanensis -Bubalus sp. -Bubo -Bubo bengalensis -Bubo bubo -Bubo scandiacus -Bubo sumatranus -Bubo virginianus -Bubulcus ibis -Bucephala albeola -Bucephala clangula -Buddleja -Buddleja crispa -Buddleja sp. -Budorcas taxicolor -Budorcas taxicolor tibetana -Buergenerula spartinae -Bufo bufo -Bufo gargarizans -Bufo spinosus -Buglossoides arvensis -Bulbophyllum -Bulinus globosus -Bupleurum -Bupleurum chinense -Burhinus grallarius -Burhinus oedicnemus -Burkholderia -Burkholderia ambifaria -Burkholderia cenocepacia -Burkholderia cenocepacia HI2424 -Burkholderia cepacia -Burkholderia contaminans -Burkholderia gladioli -Burkholderia glumae -Burkholderia pseudomallei -Burkholderia pseudomallei 1026b -Burkholderia pseudomallei 9 -Burkholderia pseudomallei K96243 -Burkholderia pseudomallei NCTC 13178 -Burkholderia pyrrocinia -Burkholderia thailandensis -Burkholderiales -Burmoniscus okinawaensis -Busseola fusca -Butastur indicus -Buteo -Buteo brachyurus -Buteo buteo -Buteo buteo vulpinus -Buteo jamaicensis -Buteo japonicus -Buteo lagopus lagopus -Buteo lineatus -Buteo platypterus -Buteo regalis -Buteo rufinus -Buteo rufinus rufinus -Buteo rufofuscus -Buteo swainsoni -Buteogallus meridionalis -Butorides striata -Butorides virescens -Buttiauxella -Butyrivibrio fibrisolvens DSM 3071 -Buxbaumia aphylla -Bycanistes fistulator sharpii -Byrsonima crassifolia -Cabillus tongarevae -Cacajao melanocephalus -Cacajao rubicundus -Cacatua -Cacatua alba -Cacatua ducorpsii -Cacatua galerita -Cacatua galerita eleonora -Cacatua galerita triton -Cacatua goffiniana -Cacatua haematuropygia -Cacatua moluccensis -Cacatua ophthalmica -Cacatua pastinator -Cacatua sanguinea -Cacatua sulphurea -Cacatua tenuirostris -Cacatuidae -Cactaceae -Cadra cautella -Caenorhabditis brenneri -Caenorhabditis briggsae -Caenorhabditis elegans -Caesalpinia -Cafeteria roenbergensis -Cairina moschata -Cajanus cajan -Cajanus scarabaeoides -Cakile maritima -Caladenia latifolia -Caladium -Caladium bicolor -Calandrella cinerea -Calanoida -Calanthe -Calanthe discolor -Calanthe flava -Calanthe sylvatica -Calanthe triplicata -Calceolaria -Caldibacillus debilis GB1 -Calendula -Calendula arvensis -Calendula officinalis -Calibrachoa -Calicophoron daubneyi -Calidris -Calidris acuminata -Calidris alba -Calidris alpina -Calidris canutus -Calidris ferruginea -Calidris fuscicollis -Calidris mauri -Calidris minuta -Calidris minutilla -Calidris ptilocnemis -Calidris pusilla -Calidris ruficollis -Calidris temminckii -Caligus clemensi -Caligus rogercresseyi -Calla -Callianthe picta -Callianthe sellowiana -Callianthe striata -Callicarpa -Callicarpa americana -Callicarpa dichotoma -Callicebus -Callicebus nigrifrons -Callicebus personatus -Callicebus sp. -Calliergon cordifolium -Callimico goeldii -Callinectes arcuatus -Callinectes danae -Callinectes ornatus -Callinectes sapidus -Callionymus kaianus -Calliope calliope -Calliphora augur -Calliphora vicina -Calliphoridae -Callistephus -Callistephus chinensis -Calliteara pudibunda -Callithrix -Callithrix geoffroyi -Callithrix jacchus -Callithrix penicillata -Callithrix sp. -Callocephalon fimbriatum -Callochromis macrops -Callochromis pleurospilus -Callonetta leucophrys -Callorhinus ursinus -Callosciurus erythraeus -Callosciurus erythraeus thaiwanensis -Callosciurus finlaysonii -Callosciurus notatus -Callosciurus prevostii -Caloenas nicobarica -Calomys callidus -Calomys callosus -Calomys fecundus -Calomys laucha -Calomys musculinus -Calomys sp. -Calomys tener -Calopogonium mucunoides -Caloptilia theivora -Caloscypha fulgens -Calotes versicolor -Calotriton asper -Calotropis -Calotropis gigantea -Calotropis procera -Caluromys -Caluromys philander -Calvadosia cruxmelitensis -Calypogeia fissa -Calypte anna -Calypte costae -Calyptocarpus vialis -Calyptorhynchus banksii -Calyptorhynchus lathami -Calystegia -Calystegia hederacea -Calystegia sepium -Camarhynchus pallidus -Camelina sativa -Camellia -Camellia japonica -Camellia oleifera -Camellia reticulata -Camellia sinensis -Camelus -Camelus bactrianus -Camelus dromedarius -Campanula takesimana -Campodea augens -Campodea silvestrii -Campoletis chlorideae -Campoletis sonorensis -Camponotus -Camponotus japonicus -Camponotus yamaokai -Campsis radicans -Campylobacter -Campylobacter coli -Campylobacter jejuni -Campylobacter jejuni RM1221 -Campylobacter jejuni subsp. jejuni -Campylobacter jejuni subsp. jejuni 00-2425 -Campylobacter sp. -Campylospermum duparquetianum -Canavalia ensiformis -Canavalia sp. -Candidatus Arsenophonus arthropodicus -Candidatus Azobacteroides pseudotrichonymphae -Candidatus Hamiltonella -Candidatus Hamiltonella defensa -Candidatus Helarchaeota -Candidatus Liberibacter asiaticus -Candidatus Liberibacter asiaticus str. psy62 -Candidatus Lokiarchaeia -Candidatus Lokiarchaeota -Candidatus Megaira polyxenophila -Candidatus Odinarchaeum yellowstonii -Candidatus Pelagibacter -Candidatus Pelagibacter sp. FZCC0015 -Candidatus Pelagibacter sp. HTCC7211 -Candidatus Pelagibacter ubique HTCC1062 -Candidatus Poseidoniales -Candidatus Puniceispirillum marinum IMCC1322 -Candidatus Xenohaliotis californiensis -Canidae -Canis -Canis adustus -Canis aureus -Canis latrans -Canis lupus -Canis lupus baileyi -Canis lupus familiaris -Canis lupus lupus -Canis lupus nubilus -Canis lupus signatus -Canis mesomelas -Canis simensis -Canis sp. -Canna -Canna indica -Canna paniculata -Canna x generalis -Cannabaceae -Cannabis sativa -Cannabis sativa subsp. sativa -Canthigaster rivulata -Capillidium adiaeretum -Capillidium heterosporum -Capitulum mitella -Capparis spinosa -Capra -Capra aegagrus -Capra caucasica -Capra hircus -Capra ibex -Capra nubiana -Capra pyrenaica -Capra sibirica -Capra sp. -Capraria biflora -Capreolus capreolus -Capreolus pygargus -Capricornis -Capricornis crispus -Capricornis milneedwardsii -Caprifoliaceae -Caprimulgus europaeus -Caprinae -Capsaspora owczarzaki ATCC 30864 -Capsella bursa-pastoris -Capsicum -Capsicum annuum -Capsicum annuum var. annuum -Capsicum annuum var. glabriusculum -Capsicum assamicum -Capsicum baccatum -Capsicum baccatum var. pendulum -Capsicum chinense -Capsicum chinense x Capsicum frutescens -Capsicum coccineum -Capsicum frutescens -Capsicum pubescens -Caracal -Caracal caracal -Caracara plancus -Carangoides equula -Carassius auratus -Carassius carassius -Carassius gibelio -Carcinus maenas -Cardinalis -Cardinalis cardinalis -Cardioderma cor -Cardiospermum microcarpum -Carduelis carduelis -Carduus -Carduus bourgaeanus -Caretta caretta -Carica papaya -Caridea -Cariniana estrellensis -Carios pusillus -Carios vespertilionis -Carissa -Carnegiea gigantea -Carnivora -Carnobacterium divergens -Carollia brevicauda -Carollia perspicillata -Carollia sowelli -Carpesium abrotanoides -Carpinus betulus -Carpiodes cyprinus -Carpodacus erythrinus -Carpodacus roseus -Carpodacus sibiricus -Carpotroche brasiliensis -Carteria obtusa -Carthamus tinctorius -Carya cordiformis -Carya illinoinensis -Casinycteris argynnis -Cassia -Castalius rosimon -Castanea crenata -Castanea mollissima -Castanea sativa -Castanea sativa x Castanea crenata -Castor canadensis -Castor fiber -Castor fiber albicus -Castoridae -Catenulispora -Catharanthus roseus -Cathartes aura -Catharus fuscescens -Catharus guttatus -Catharus ustulatus -Catopsilia pomona -Catostomus commersonii -Cattleya -Cattleya x hybrida -Caulobacter -Caulobacter segnis -Caulobacter sp. -Caulobacter vibrioides -Caulobacter vibrioides CB15 -Caulobacter vibrioides NA1000 -Causonis japonica -Cavia aperea -Cavia porcellus -Cebidae -Cebuella pygmaea -Cebus -Cebus albifrons -Cebus capucinus -Cebus imitator -Cebus sp. -Cecropia hololeuca -Cecropis daurica -Cedecea davisae -Ceiba pentandra -Celatoblatta -Celeribacter marinus -Cellulophaga baltica -Cellulophaga baltica NN016038 -Cellulophaga sp. -Cellulophaga sp. HaHa_2_1 -Cellulophaga sp. HaHa_2_95 -Cellulophaga sp. HaHaR_3_176 -Cellulophaga sp. MM#3 -Cellulophaga sp. NN014847 -Cellulosimicrobium sp. -Celmisia lyallii -Celonites abbreviatus -Celosia -Celosia argentea var. plumosa -Celosia cristata -Cenchrus americanus -Cenchrus ciliaris -Cenchrus clandestinus -Cenchrus compressus -Cenchrus echinatus -Cenchrus flaccidus -Cenchrus myosuroides -Cenchrus purpureus -Cenchrus sp. -Cenchrus unisetus -Cenostigma pluviosum -Centella asiatica -Centranthus ruber -Centratherum punctatum -Centroberyx rubricaudus -Centrochelys sulcata -Centropristis striata -Centrosema brasilianum -Centrosema pubescens -Centrotus cornutus -Centruroides sculpturatus -Cephalophinae -Cephalopholis argus -Cephalopholis boenak -Cephalopholis spiloparaea -Cephalopholis urodeta -Cephalophorus rufilatus -Cephalotaxus hainanensis -Cephalotaxus harringtonia -Cephalotermes -Cephus spinipes -Cepora nerissa -Ceraphron -Ceraphron sp. AD-2014 -Cerapteryx graminis -Cerastes cerastes -Cerastium glomeratum -Ceratina chalcites -Ceratina chalybea -Ceratina cucurbitina -Ceratina dentiventris -Ceratina gravidula -Ceratitis capitata -Ceratobasidium cereale -Ceratobasidium sp. -Ceratocystis cacaofunesta -Ceratocystis fimbriata -Ceratophyllus gallinae -Ceratopogonidae -Ceratorhiza oryzae-sativae -Ceratosolen emarginatus -Ceratosolen solmsi -Ceratotherium simum -Cerceris -Cercis -Cercis canadensis -Cercocebus -Cercocebus agilis -Cercocebus atys -Cercocebus torquatus -Cercocebus torquatus torquatus -Cercopithecidae -Cercopithecus albogularis -Cercopithecus ascanius -Cercopithecus ascanius schmidti -Cercopithecus ascanius whitesidei -Cercopithecus campbelli -Cercopithecus cephus -Cercopithecus cephus cephus -Cercopithecus denti -Cercopithecus diana -Cercopithecus erythrotis -Cercopithecus hamlyni -Cercopithecus kandti -Cercopithecus mitis -Cercopithecus mona -Cercopithecus neglectus -Cercopithecus nictitans -Cercopithecus pogonias -Cercopithecus wolfi -Cercospora beticola -Cerdocyon thous -Cereibacter sphaeroides -Cervidae -Cervidae sp. -Cervus -Cervus albirostris -Cervus canadensis -Cervus canadensis nelsoni -Cervus elaphus -Cervus elaphus barbarus -Cervus nippon -Cervus nippon nippon -Cestoda -Cestrum -Cestrum aurantiacum -Cestrum elegans -Cestrum endlicheri -Cestrum nocturnum -Cetacea -Ceyx azureus -Chaenomeles japonica -Chaenostoma cordatum -Chaerephon -Chaerephon aloysiisabaudiae -Chaerephon leucogaster -Chaerephon plicatus -Chaerephon pusillus -Chaetoceros curvisetus -Chaetoceros debilis -Chaetoceros lorenzianus -Chaetoceros salsugineus -Chaetoceros setoense -Chaetoceros sp. -Chaetoceros sp. SS628-11 -Chaetoceros sp. TG07-C28 -Chaetoceros tenuissimus -Chaetocoelopa sydneyensis -Chaetodipus -Chaetodipus baileyi -Chaetodipus hispidus -Chaetodipus penicillatus -Chaetodipus spinatus -Chaetodon bennetti -Chaetura pelagica -Chaeturichthys stigmatias -Chalcides ocellatus -Chalcocoris rutilans -Chalinochromis brichardi -Chalinolobus gouldii -Chalinolobus morio -Chalinolobus tuberculatus -Chaliopsis junodi -Chalybion californicum -Chamaecyparis lawsoniana -Chamaedorea elegans -Chamaeleo calyptratus -Chamaeleonidae -Chamaenerion angustifolium -Chamaescilla corymbosa -Channa argus -Channa lucius -Channa micropeltes -Channa striata -Channidae -Chanodichthys erythropterus -Chanos chanos -Chaoborus -Chaoborus americanus -Chaoborus trivitattus -Chara australis -Charadriiformes -Charadrius melodus -Charadrius ruficapillus -Charybdis -Charybdis japonica -Chasiempis sandwichensis -Chauliodes -Chauna torquata -Cheilinus trilobatus -Cheilodipterus quinquelineatus -Cheilomenes sexmaculata -Cheilopogon heterurus -Chelidonichthys cuculus -Chelidonichthys lucerna -Chelidonium majus -Chelidoperca -Chelidoperca sp. -Chelon auratus -Chelon labrosus -Chelonia mydas -Chelonoidis carbonarius -Chelonus inanitus -Chelostoma campanularum -Chelostoma florisomne -Chelostoma rapunculi -Chelydra serpentina -Chengiodendron matsumuranum -Chenonetta jubata -Chenopodiastrum murale -Chenopodium -Chenopodium album -Chenopodium amaranticolor -Chenopodium opulifolium -Chenopodium quinoa -Cherax quadricarinatus -Chersina angulata -Chilabothrus inornatus -Chilo suppressalis -Chimaera sp. -Chinchilla lanigera -Chionochloa macra -Chionochloa rubra -Chionoecetes bairdi -Chironectes minimus -Chironomidae -Chironomus decorus -Chironomus thummi -Chironomus zealandicus -Chiropotes sp. -Chiroptera -Chiroptera sp. -Chlamydera cerviniventris -Chlamydia -Chlamydia abortus -Chlamydia pneumoniae AR39 -Chlamydia psittaci -Chlamydotis -Chlamydotis macqueenii -Chlamydotis undulata -Chlidonias hybrida -Chlidonias leucopterus -Chloebia gouldiae -Chloephaga picta -Chloephaga poliocephala -Chlorarachnion reptans -Chlorella -Chlorella heliozoae -Chlorella variabilis -Chlorella vulgaris -Chlorion hirtum -Chloris chloris -Chloris gayana -Chlorobiaceae bacterium -Chlorocalymma cryptacanthum -Chlorocebus -Chlorocebus aethiops -Chlorocebus cynosuros -Chlorocebus pygerythrus -Chlorocebus sabaeus -Chlorocebus tantalus -Chlorodrepanis virens -Chodsigoa hypsibia -Chodsigoa smithii -Choeras sp. -Choerodon azurio -Choloepus didactylus -Choloepus hoffmanni -Chondrichthyes -Chondrocladia grandis -Chondrostereum purpureum -Chorilaena quercifolia -Choristoneura diversana -Choristoneura fumiferana -Choristoneura murinana -Choristoneura occidentalis -Choristoneura occidentalis biennis -Choristoneura retiniana -Choristoneura rosaceana -Chorthippus parallelus -Chroicocephalus brunnicephalus -Chroicocephalus cirrocephalus -Chroicocephalus genei -Chroicocephalus maculipennis -Chroicocephalus novaehollandiae -Chroicocephalus ridibundus -Chroicocephalus scopulinus -Chromohalobacter -Chromolaena odorata -Chrozophora hierosolymitana -Chrozophora tinctoria -Chrysanthemum -Chrysanthemum boreale -Chrysanthemum indicum -Chrysanthemum sp. -Chrysanthemum x morifolium -Chrysanthemum yoshinaganthum -Chrysanthemum zawadskii var. latilobum -Chrysemys picta picta -Chryseobacterium indologenes -Chrysis fasciata -Chrysis gracillima -Chrysochromulina -Chrysochromulina parva -Chrysocyon brachyurus -Chrysodeixis acuta -Chrysodeixis chalcites -Chrysodeixis includens -Chrysolophus amherstiae -Chrysolophus pictus -Chrysomelidae -Chrysomya megacephala -Chrysomya rufifacies -Chrysomya varipes -Chrysopidae -Chrysotila carterae -Chrysura austriaca -Chrysura cuprea -Chrysura radians -Chyphotes -Cicadella viridis -Cicer arietinum -Cichla ocellaris -Cichorium endivia -Cichorium intybus -Ciconia boyciana -Ciconia ciconia -Ciconiidae -Cimex adjunctus -Cimex hemipterus -Cimex lectularius -Cinclus cinclus -Cineraria -Cinnamomum chago -Cipangopaludina cathayensis -Circus aeruginosus -Circus cyaneus -Cirripedia -Cirsium -Cirsium setidens -Cistus incanus -Cistus salviifolius -Citrobacter -Citrobacter amalonaticus -Citrobacter braakii -Citrobacter freundii -Citrobacter koseri -Citrobacter portucalensis -Citrobacter rodentium -Citrobacter sp. -Citrobacter sp. TM1552 -Citromicrobium bathyomarinum -Citromicrobium sp. RCC1878 -Citrullus -Citrullus colocynthis -Citrullus lanatus -Citrullus lanatus subsp. vulgaris -Citrus -Citrus aurantiifolia -Citrus aurantiifolia x Citrus japonica var. margarita -Citrus aurantium -Citrus australasica -Citrus bergamia -Citrus cavaleriei -Citrus clementina -Citrus daoxianensis -Citrus deliciosa -Citrus hybrid -Citrus hybrid cultivar -Citrus hystrix -Citrus jambhiri -Citrus japonica -Citrus japonica var. margarita -Citrus junos -Citrus limetta -Citrus limettioides -Citrus limon -Citrus limonia -Citrus macrophylla -Citrus macroptera -Citrus madurensis -Citrus maxima -Citrus medica -Citrus meyeri -Citrus myrtifolia -Citrus nobilis -Citrus reshni -Citrus reticulata -Citrus reticulata x Citrus sinensis -Citrus sinensis -Citrus sinensis x Citrus reticulata -Citrus sinensis x Citrus trifoliata -Citrus sp. -Citrus tamurana -Citrus tankan -Citrus trifoliata -Citrus unshiu -Citrus unshiu x Citrus sinensis -Citrus volkameriana -Citrus wilsonii -Citrus x latifolia -Citrus x microcarpa -Citrus x paradisi -Citrus x paradisi x Citrus trifoliata -Citrus x tangelo -Civettictis civetta -Cladocera -Cladocopium sp. C1 -Cladonia arbuscula -Cladorhiza oxeata -Cladosporium cladosporioides -Cladosporium ramotenellum -Cladosporium tenuissimum -Clanga pomarina -Clangula hyemalis -Clanis bilineata -Clarireedia homoeocarpa -Clavibacter michiganensis -Clavibacter michiganensis subsp. michiganensis -Clavibacter michiganensis subsp. nebraskensis -Cleisostoma racemiferum -Cleistocactus winteri -Cleithracara maronii -Clematis -Clematis apiifolia -Clematis brevicaudata -Clematis sp. -Clematis vitalba -Cleome -Cleome affinis -Clerodendrum -Clerodendrum bungei -Clerodendrum cyrtophyllum -Clerodendrum philippinum -Clerodendrum sp. -Clerodendrum speciosum -Clerodendrum trichotomum -Clerodendrum umbellatum -Clethrionomys gapperi -Cletus punctiger -Climacium dendroides -Clitocybe odora -Clitoria ternatea -Clivia miniata -Clogmia albipunctata -Clohesyomyces aquaticus -Clonorchis sinensis -Clostera anachoreta -Clostera anastomosis -Clostridioides -Clostridioides difficile -Clostridioides sp. ES-S-0107-01 -Clostridioides sp. ES-S-0173-01 -Clostridium -Clostridium beijerinckii -Clostridium botulinum -Clostridium botulinum D -Clostridium botulinum D str. 1873 -Clostridium butyricum -Clostridium perfringens -Clostridium perfringens ATCC 13124 -Clostridium perfringens SM101 -Clostridium saccharoperbutylacetonicum N1-4(HMT) -Clostridium sporogenes -Clostridium tetani -Clostridium tetani ATCC 9441 -Clupanodon thrissa -Clupea harengus -Clupea pallasii -Clupeidae -Cnaphalocrocis medinalis -Cnephasia longana -Cnidium officinale -Cnidoscolus aconitifolius -Cnidoscolus chayamansa -Cnidoscolus urens -Coccinia grandis -Coccoidea -Coccolithus braarudii -Coccothraustes coccothraustes -Cocos nucifera -Codiaeum variegatum -Codonopsis lanceolata -Codonopsis pilosula -Coelastrella sp. UTEX B 3026 -Coelioxys conoidea -Coelorinchus multispinulosus -Coendou prehensilis -Coendou spinosus -Coenobiodes granitalis -Coffea -Coilia mystus -Coix lacryma-jobi -Colaptes auratus -Colaptes campestris -Colchicum autumnale -Coleoptera -Coleura -Coleura afra -Coleura kibomalandy -Coleus -Coleus amboinicus -Coleus scutellarioides -Colias croceus -Colinus virginianus -Colinus virginianus ridgwayi -Colletes sp. -Colletotrichum -Colletotrichum acutatum -Colletotrichum camelliae -Colletotrichum caudatum -Colletotrichum curcumae -Colletotrichum eremochloae -Colletotrichum falcatum -Colletotrichum fructicola -Colletotrichum gloeosporioides -Colletotrichum higginsianum -Colletotrichum liriopes -Colletotrichum navitas -Colletotrichum sp. -Colletotrichum truncatum -Colletotrichum zoysiae -Colobopsis nipponica -Colobopsis shohki -Colobus -Colobus angolensis -Colobus guereza -Colobus polykomos -Colocasia -Colocasia esculenta -Coloeus monedula -Coloradia pandora -Colpa sexmaculata -Columba -Columba guinea -Columba livia -Columba oenas -Columba palumbus -Columba pulchricollis -Columba sp. -Columbidae -Columbidae sp. -Columbiformes -Columnea -Colwellia -Combretum confertum -Commelina -Commelina benghalensis -Commelina communis -Commelina cyanea -Commelina diffusa -Commelina erecta -Condylorrhiza vestigialis -Conepatus -Conepatus leuconotus -Conger japonicus -Conidiobolus chlamydosporus -Conidiobolus lamprauges -Conidiobolus sp. -Coniella diplodiella -Conium -Conium maculatum -Connochaetes -Connochaetes taurinus -Connochaetes taurinus taurinus -Conocephalus -Conocephalus chinensis -Conocephalus maculatus -Conocephalus melaenus -Conolophus subcristatus -Conopophaga aurita -Consolea spinosissima -Constrictotermes -Conticribra weissflogii -Contopus sordidulus -Convolvulus -Convolvulus arvensis -Convolvulus humilis -Conyza bonariensis -Conyza sp. -Coprosma repens -Copsychus -Copsychus malabaricus -Copsychus saularis -Coptotermes acinaciformis -Coptotermes formosanus -Coptotermes gestroi -Coptotermes sp. -Coquillettidia -Coquillettidia albicosta -Coquillettidia fuscopennata -Coquillettidia juxtamansonia -Coquillettidia linealis -Coquillettidia lynchi -Coquillettidia maculipennis -Coquillettidia metallica -Coquillettidia nigricans -Coquillettidia perturbans -Coquillettidia richiardii -Coquillettidia venezuelensis -Coquillettidia xanthogaster -Coracias garrulus -Coraciidae -Coracopsis vasa -Coragyps atratus -Corallus annulatus -Corallus caninus -Corallus hortulanus -Corchoropsis tomentosa -Corchorus -Corchorus capsularis -Corchorus hirtus -Corchorus olitorius -Corchorus siliquosus -Corchorus tridens -Corcyra cephalonica -Cordulegaster boltonii -Cordyceps chanhua -Cordyceps javanica -Cordyline fruticosa -Cordylus tropidosternum -Coregonus -Coregonus lavaretus -Coregonus migratorius -Coreopsis auriculata -Coreopsis basalis -Coriandrum sativum -Corixidae -Cornitermes -Cornus -Cornus florida -Corvidae -Corvus -Corvus bennetti -Corvus brachyrhynchos -Corvus caurinus -Corvus corax -Corvus cornix -Corvus corone -Corvus coronoides -Corvus frugilegus -Corvus hawaiiensis -Corvus macrorhynchos -Corvus ossifragus -Corvus splendens -Corydalidae -Corydalis speciosa -Corydalus cornutus -Corylus -Corylus avellana -Corynactis australis -Corynandra viscosa -Corynebacterium -Corynebacterium diphtheriae -Corynebacterium flavescens -Corynebacterium glutamicum -Corynebacterium glutamicum MB001 -Corynebacterium pseudotuberculosis -Corynebacterium pseudotuberculosis 31 -Corynebacterium simulans -Corynebacterium vitaeruminis -Corynebacterium xerosis -Corynespora cassiicola -Corynocarpus laevigatus -Corynorhinus rafinesquii -Corynorhinus townsendii -Coryphospingus pileatus -Corythornis cristatus -Coscoroba coscoroba -Cosmocalanus darwinii -Cosmocomoidea morrilli -Cossypha albicapillus -Cossypha niveicapilla -Costora delora -Costus spiralis -Cotesia glomerata -Cotesia rubecula -Cotesia sesamiae -Cotesia sp. -Cotesia vestalis -Cotoneaster microphyllus -Cottocomephorus grewingki -Coturnix -Coturnix coturnix -Coturnix japonica -Coturnix sp. -Cotyledon orbiculata -Cracticus torquatus -Crambe hispanica subsp. abyssinica -Crambus -Crangon -Crangon crangon -Crassocephalum crepidioides -Crassostrea ariakensis -Crassostrea gigas -Crataegus -Crataegus monogyna -Crataegus pinnatifida -Craterocephalus stercusmuscarum fulvus -Craugastor ranoides -Crax fasciolata -Crematogaster mimosae -Crematogaster nigriceps -Crepidiastrum denticulatum -Cricetidae -Cricetinae -Cricetomys -Cricetomys emini -Cricetomys gambianus -Cricetulus barabensis -Cricetulus griseus -Cricetulus longicaudatus -Cricetulus migratorius -Cricetulus sokolovi -Cricetus cricetus -Crinum -Crinum asiaticum -Crithagra mozambica -Crithidia -Crithidia abscondita -Crithidia otongatchiensis -Crocallis elinguaria -Croceibacter atlanticus HTCC2559 -Crocidura -Crocidura attenuata -Crocidura douceti -Crocidura dracula -Crocidura goliath -Crocidura grandiceps -Crocidura hirta -Crocidura lasiura -Crocidura leucodon -Crocidura littoralis -Crocidura luna -Crocidura montis -Crocidura obscurior -Crocidura olivieri -Crocidura russula -Crocidura shantungensis -Crocidura somalica -Crocidura tanakae -Crocidura theresae -Crocodilurus amazonicus -Crocodylidae -Crocodylus johnsoni -Crocodylus moreletii -Crocodylus niloticus -Crocodylus porosus -Crocodylus siamensis -Crocothemis servilia -Crocus -Crocus almehensis -Crocus kotschyanus subsp. kotschyanus -Crocus sativus -Crocuta crocuta -Cromileptes altivelis -Cronartium ribicola -Cronobacter -Cronobacter dublinensis -Cronobacter malonaticus LMG 23826 -Cronobacter sakazakii -Cronobacter sp. -Cronobacter turicensis -Crossandra infundibuliformis -Crossoptilon auritum -Crossorhombus sp. -Crotalaria -Crotalaria juncea -Crotalaria micans -Crotalaria paulina -Crotalaria retusa -Crotalaria spectabilis -Crotalus atrox -Crotalus catalinensis -Crotalus cerastes -Crotalus durissus -Crotalus durissus terrificus -Crotalus horridus -Crotalus lepidus -Crotalus lepidus klauberi -Crotalus mitchellii -Crotalus molossus molossus -Crotalus molossus nigrescens -Crotalus scutulatus -Croton -Croton bonplandianus -Croton glandulosus -Croton hirtus -Croton malvaviscifolius -Crotophaga ani -Crustacea -Crustacea sp. 'Maxillopoda' -Cryphonectria carpinicola -Cryphonectria naterciae -Cryphonectria nitschkei -Cryphonectria parasitica -Cryphonectria radicalis -Cryphonectria sp. -Cryptoblepharus virgatus -Cryptocercus wrighti -Cryptophlebia peltastica -Cryptosporidium parvum -Cryptosporidium sp. -Cryptotaenia japonica -Cryptotermes secundus -Ctenocephalides felis -Ctenodactylus gundi -Ctenolabrus rupestris -Ctenopharyngodon idella -Ctenophorus nuchalis -Cucumaria miniata -Cucumis -Cucumis anguria -Cucumis dipsaceus -Cucumis maderaspatanus -Cucumis melo -Cucumis melo subsp. agrestis -Cucumis melo var. cantalupo -Cucumis melo var. conomon -Cucumis melo var. dudaim -Cucumis melo var. flexuosus -Cucumis melo var. inodorus -Cucumis melo var. makuwa -Cucumis melo var. momordica -Cucumis melo var. saccharinus -Cucumis metulifer -Cucumis sativus -Cucurbita -Cucurbita argyrosperma -Cucurbita foetidissima -Cucurbita maxima -Cucurbita moschata -Cucurbita pepo -Cucurbita pepo subsp. ovifera -Cucurbita pepo var. melopepo -Cucurbita pepo var. ozarkana -Cucurbita pepo var. texana -Cucurbitaceae -Culex -Culex (Lophoceraomyia) sp. -Culex accelerans -Culex aikenii -Culex amazonensis -Culex annulioris -Culex annulirostris -Culex annulus -Culex antennatus -Culex apicinus -Culex australicus -Culex bitaeniorhynchus -Culex cedecei -Culex chidesteri -Culex cinereus -Culex coronator -Culex decens -Culex declarator -Culex delpontei -Culex dunni -Culex edwardsi -Culex epanatasis -Culex epidesmus -Culex erraticus -Culex erythrothorax -Culex fuscocephala -Culex gelidus -Culex globocoxitus -Culex gnomatos -Culex guiarti -Culex idottus -Culex impudicus -Culex inatomii -Culex interfor -Culex interrogator -Culex iolambdis -Culex lactator -Culex laticinctus -Culex maxi -Culex modestus -Culex mollis -Culex neavei -Culex nebulosus -Culex nigripalpus -Culex ocossa -Culex orientalis -Culex pallidothorax -Culex paracrybda -Culex perexiguus -Culex perfuscus -Culex pipiens -Culex pipiens complex -Culex pipiens molestus -Culex pipiens pallens -Culex pipiens pipiens -Culex pipiens sensu lato -Culex poicilipes -Culex portesi -Culex pruina -Culex pseudovishnui -Culex pullus -Culex quinquefasciatus -Culex restuans -Culex rubinotus -Culex salinarius -Culex sasai -Culex simpliciforceps -Culex simpsoni -Culex sitiens -Culex sp. -Culex spissipes -Culex squamosus -Culex stigmatosoma -Culex taeniopus -Culex tarsalis -Culex telesilla -Culex territans -Culex terzii -Culex theileri -Culex thriambus -Culex torrentium -Culex tritaeniorhynchus -Culex univittatus -Culex vagans -Culex vansomereni -Culex vishnui -Culex vomerifer -Culex whitmorei -Culex zombaensis -Culicidae -Culicinae -Culicoidea -Culicoides -Culicoides arakawae -Culicoides austropalpalis -Culicoides brevitarsis -Culicoides cataneii -Culicoides circumscriptus -Culicoides dycei -Culicoides haranti -Culicoides histrio -Culicoides imicola -Culicoides insignis -Culicoides jacobsoni -Culicoides longipennis -Culicoides maculatus -Culicoides marksi -Culicoides newsteadi -Culicoides obsoletus -Culicoides orientalis -Culicoides oxystoma -Culicoides paraensis -Culicoides peregrinus -Culicoides punctatus -Culicoides puncticollis -Culicoides schultzei -Culicoides sonorensis -Culicoides stellifer -Culicoides submaritimus -Culicoides tainanus -Culicoides univittatus -Culicoides variipennis -Culiseta -Culiseta annulata -Culiseta incidens -Culiseta inornata -Culiseta longiareolata -Culiseta melanura -Culiseta minnesotae -Culiseta morsitans -Culiseta particeps -Cuminum cyminum -Cuniculus -Cuniculus paca -Curculio bimaculatus -Curculionidae -Curcuma alismatifolia -Curcuma longa -Curio rowleyanus -Curruca conspicillata -Curruca curruca -Curtobacterium -Curtobacterium sp. -Curvibacter -Curvibacter sp. AEP1.3 -Curvularia protuberata -Curvularia sp. -Cuscuta -Cuscuta reflexa -Cuterebra austeni -Cutibacterium acnes -Cutibacterium acnes subsp. acnes -Cutibacterium acnes subsp. defendens ATCC 11828 -Cyamopsis tetragonoloba -Cyanistes caeruleus -Cyanobacteriota -Cyanocitta -Cyanocitta cristata -Cyanoliseus patagonus bloxami -Cyanopica cyanus -Cyanoramphus auriceps -Cyanoramphus novaezelandiae -Cyanoramphus saisseti -Cyanthillium cinereum -Cyathopharynx furcifer -Cyathus bulleri -Cybaeus signifer -Cybister lateralimarginalis -Cycadopsida -Cycas revoluta -Cyclamen -Cyclamen persicum -Cyclopia genistoides -Cyclopodia greeffi -Cyclopterus lumpus -Cyclosorus interruptus -Cydia pomonella -Cydistomyia duplonotata -Cydonia -Cydonia oblonga -Cygnus -Cygnus atratus -Cygnus bewickii -Cygnus buccinator -Cygnus columbianus -Cygnus columbianus jankowskii -Cygnus cygnus -Cygnus melancoryphus -Cygnus olor -Cylindropuntia -Cylindropuntia arbuscula -Cylindropuntia echinocarpa -Cylindropuntia ramosissima -Cylindropuntia spinosior -Cylindropuntia whipplei -Cylindrospermopsis raciborskii -Cylindrospermopsis raciborskii KLL07 -Cylindrotheca closterium -Cymatogaster aggregata -Cymbidium -Cymbidium dayanum -Cymbidium elegans -Cymbidium ensifolium -Cymbidium faberi -Cymbidium goeringii -Cymbidium hookerianum -Cymbidium hybrid cultivar -Cymbidium kanran -Cymbidium lancifolium -Cymbidium pendulum -Cymbidium sinense -Cymbidium tortisepalum -Cymbopogon citratus -Cymbopogon flexuosus -Cymbopogon martinii -Cymbopogon schoenanthus -Cymbopogon winterianus -Cymodocea nodosa -Cynanchum chinense -Cynanchum rostellatum -Cynanchum wilfordii -Cynara cardunculus -Cynara cardunculus var. scolymus -Cynictis penicillata -Cynodon -Cynodon dactylon -Cynodon dactylon x Cynodon transvaalensis -Cynodon nlemfuensis -Cynodon transvaalensis x Cynodon dactylon -Cynoglossus semilaevis -Cynoglossus sp. -Cynomops -Cynomops abrasus -Cynomops planirostris -Cynomys -Cynomys gunnisoni -Cynomys ludovicianus -Cynops orientalis -Cynopterus brachyotis -Cynopterus horsfieldii -Cynopterus sp. -Cynopterus sphinx -Cynosarga ornata -Cynosurus cristatus -Cynosurus echinatus -Cyperus difformis -Cyperus esculentus -Cyperus rotundus -Cyphomyrmex -Cyprichromis -Cyprichromis microlepidotus -Cyprichromis sp. 'dwarf jumbo' AB-2019 -Cyprinidae -Cyprinus carpio -Cyprinus carpio 'koi' -Cyprinus carpio carpio -Cyprinus carpio haematopterus -Cyprinus carpio nudus -Cyprinus rubrofuscus -Cypripedium franchetii -Cypripedium parviflorum -Cypseloides niger -Cyrtanthus elatus -Cystophora cristata -Cytobacillus firmus DS1 -Cytobacillus oceanisediminis -Cytospora ceratosperma -Cytospora leucostoma -Cytospora ribis -Cytospora sacchari -Daboia -Dacelo novaeguineae -Dactylis glomerata -Dactyloctenium -Dactyloctenium aegyptium -Dactylonectria torresensis -Dactylorhiza incarnata -Dactylorhiza majalis -Dahlia -Dahlia coccinea -Dahlia pinnata -Dahlia rupicola -Dahlia sherffii -Dahlia sp. (in: eudicots) -Dahlia tenuicaulis -Dalechampia -Dama -Dama dama -Damaliscus lunatus jimela -Damaliscus pygargus -Danaus melanippus -Danaus plexippus -Danio rerio -Danthonia californica -Danthoniopsis petiolata -Daphne -Daphne mezereum -Daphne odora -Daphnia mendotae -Darna nararia -Darna trima -Dasineura jujubifolia -Dasychira plagiata -Dasymys incomtus -Dasymys rufulus -Dasypeltis atra -Dasypoda hirtipes -Dasypterus ega -Dasypterus intermedius -Dasypterus xanthinus -Dasypus novemcinctus -Dasyuroides byrnei -Datura -Datura inoxia -Datura leichhardtii -Datura metel -Datura stramonium -Datura stramonium var. inermis -Daucus -Daucus carota -Daucus carota subsp. carota -Daucus carota subsp. sativus -Davidia involucrata -Davidiellaceae sp. -Debaryomyces hansenii -Decapterus -Decapterus kurroides -Decapterus macarellus -Decapterus macrosoma -Decapterus russelli -Deinbollia borbonica -Deinocerites -Deinocerites atlanticus -Delftia -Delftia acidovorans -Delftia sp. 670 -Delftia tsuruhatensis -Delias eucharis -Delisea pulchra -Delitschia confertaspora -Delitschia confertaspora ATCC 74209 -Delphinapterus leucas -Delphinium -Delphinium glaucum -Delphinus capensis -Delphinus delphis -Dendroaspis jamesoni jamesoni -Dendroaspis viridis -Dendrobium -Dendrobium anosmum -Dendrobium candidum -Dendrobium densiflorum -Dendrobium moschatum -Dendrobium nobile -Dendrobium officinale -Dendrobium phalaenopsis -Dendrobium philippinense -Dendrobium smillieae -Dendrocalamus -Dendrocalamus brandisii -Dendrocalamus giganteus -Dendrocalamus hamiltonii -Dendrocalamus latiflorus -Dendrocalamus rongchengensis -Dendrocalamus sinicus -Dendrocalamus strictus -Dendrocalamus tsiangii -Dendrocalamus yunnanicus -Dendrocoelum lacteum -Dendrocopos leucotos -Dendrocopos major -Dendroctonus brevicomis -Dendroctonus ponderosae -Dendrocygna autumnalis -Dendrocygna eytoni -Dendrocygna javanica -Dendrocygna viduata -Dendrolimus kikuchii -Dendrolimus pini -Dendrolimus punctatus -Dendrolimus sibiricus -Deomys ferrugineus -Dephomys defua -Dermacentor -Dermacentor auratus -Dermacentor everestianus -Dermacentor marginatus -Dermacentor nitens -Dermacentor niveus -Dermacentor nuttalli -Dermacentor occidentalis -Dermacentor reticulatus -Dermacentor silvarum -Dermacentor variabilis -Dermanyssus gallinae -Dermaptera -Dermatophagoides farinae -Dermatophagoides pteronyssinus -Dermochelys coriacea -Dermolepida albohirtum -Deropeltis erythrocephala -Deroptyus accipitrinus -Desarmillaria ectypa -Deschampsia cespitosa -Descurainia sophia -Desmodillus auricularis -Desmodium -Desmodium glabrum -Desmodium illinoense -Desmodium paniculatum -Desmodium scorpiurus -Desmodium tortuosum -Desmodus rotundus -Desmognathus conanti -Desmognathus imitator -Desmognathus monticola -Desmognathus ocoee -Desmognathus quadramaculatus -Desmognathus santeetlah -Desulfofustis -Desulfovibrio desulfuricans -Diabrotica barberi -Diabrotica undecimpunctata -Diabrotica undecimpunctata howardi -Diabrotica virgifera virgifera -Diachasmimorpha longicaudata -Diadegma fenestrale -Diadegma insulare -Diadegma semiclausum -Diadromus pulchellus -Diaea subdola -Diaemus youngi -Dianthus -Dianthus amurensis -Dianthus barbatus -Dianthus caryophyllus -Dianthus chinensis -Dianthus plumarius -Dianthus sp. -Diaphorina citri -Diaporthe ambigua -Diaporthe ampelina -Diaporthe helianthi -Diaporthe longicolla -Diaporthe pseudophoenicicola -Diaporthe rudis -Diaporthe sp. -Diaporthe vexans -Diascia -Diatraea saccharalis -Dicentrarchus labrax -Diceros bicornis -Dichanthelium oligosanthes -Dichelobacter -Dichondra repens -Dichopogon strictus -Dickeya -Dickeya chrysanthemi -Dickeya dadantii -Dickeya dianthicola -Dickeya fangzhongdai -Dickeya solani -Dickeya solani MK10 -Dickeya sp. -Dicliptera sexangularis -Dicliptera vahliana -Dicranum scoparium -Dicrocoelium dendriticum -Dictyophorus griseus -Didelphidae -Didelphis albiventris -Didelphis aurita -Didelphis marsupialis -Didemnum sp. -Didymella sp. YH-2022a -Dieffenbachia -Digera muricata -Digitalis -Digitalis lanata -Digitalis purpurea -Digitaria -Digitaria ciliaris -Digitaria cognata -Digitaria debilis -Digitaria didactyla -Digitaria horizontalis -Digitaria sanguinalis -Digitaria setigera -Digitaria velutina -Diglyphus isaea -Digyalum oweni -Dikerogammarus haemobaphes -Dimocarpus longan -Dimorphotheca -Dimorphotheca caulescens -Dimorphotheca sinuata -Dinebra chinensis -Dinematichthys -Dineutus -Dinocampus coccinellae -Dinophysis acuminata -Dinoroseobacter shibae -Diodia -Diodia virginiana -Diogenes edwardsii -Diomedea exulans -Diomedea sanfordi -Dione juno -Dione vanillae -Diopsittaca nobilis -Diopsittaca nobilis cumanensis -Dioscorea -Dioscorea abyssinica -Dioscorea alata -Dioscorea bulbifera -Dioscorea cayenensis -Dioscorea cayenensis subsp. rotundata -Dioscorea communis -Dioscorea composita -Dioscorea dumetorum -Dioscorea esculenta -Dioscorea japonica -Dioscorea nummularia -Dioscorea oppositifolia -Dioscorea parviflora -Dioscorea pentaphylla -Dioscorea polystachya -Dioscorea praehensilis -Dioscorea sansibarensis -Dioscorea schimperiana -Dioscorea transversa -Dioscorea trifida -Dioscorea zingiberensis -Diospyros -Diospyros kaki -Diospyros virginiana -Dioxys cincta -Diphlebia lestoides -Diphylla ecaudata -Diplacodes bipunctata -Diploderma splendidum -Diplodia mutila -Diplodia scrobiculata -Diplodia seriata -Diplodus sargus -Diplodus vulgaris -Diplonychus rusticus -Diplopoda -Diplotaxis erucoides -Diplotaxis tenuifolia -Dipodillus dasyurus -Dipodomys merriami -Dipodomys ordii -Dipodomys simulans -Dipodomys spectabilis -Diporeia -Diporeia hoyi -Dipsacus fullonum -Dipseliopoda -Diptera -Dipus sagitta -Dischisma capitatum -Discula destructiva -Disocactus flagelliformis -Disporopsis fuscopicta -Distimake aegyptius -Distimake dissectus -Distimake quinquefolius -Ditrema temminckii -Dittrichia viscosa -Diuris -Diuris corymbosa -Diuris longifolia -Diuris maculata -Diuris magnifica -Diuris orientis -Diuris pedunculata -Diversispora versiformis -Dobsonia exoleta -Dobsonia moluccensis -Dolichogenidea sp. -Dolichos -Dolichotis patagonum -Dolycoris baccarum -Dopasia gracilis -Dorea -Dorosoma cepedianum -Dorylus sp. -Doryrhina cyclops -Dothideomycetes sp. -Dracaena braunii -Dracaena guianensis -Dracaena sanderiana -Dracocephalum moldavica -Dracula astuta -Drakaea elastica -Drakaea livida -Drechslerella stenobrocha -Dremomys pernyi -Dremomys rufigenis fuscus -Drilus concolor -Dromaius novaehollandiae -Drosophila -Drosophila affinis -Drosophila americana -Drosophila ananassae -Drosophila biauraria -Drosophila bipectinata -Drosophila busckii -Drosophila falleni -Drosophila immigrans -Drosophila innubila -Drosophila kikkawai -Drosophila mauritiana -Drosophila melanogaster -Drosophila montana -Drosophila munda -Drosophila neotestacea -Drosophila obscura -Drosophila pseudoobscura -Drosophila repleta -Drosophila simulans -Drosophila sturtevanti -Drosophila subobscura -Drosophila subsilvestris -Drosophila suzukii -Drosophila tenebrosa -Drosophila tristis -Drosophila unispina -Drosophila virilis -Drosophilidae -Drosophilidae sp. -Drymotoxeres pucheranii -Dryobates minor -Dryomys nitedula -Dryophytes cinereus -Ducula bicolor -Dufourea dentiventris -Dugesia japonica -Dumetella -Dumetella carolinensis -Dunaliella viridis -Duranta -Duranta erecta -Dusicyon -Duttaphrynus melanostictus -Dyacopterus spadiceus -Dypsis lutescens -Dysaphis plantaginea -Dysdera crocata -Dysphania ambrosioides -Dysphania botrys -Ecballium -Ecballium elaterium -Echelus uropterus -Echinacea purpurea -Echinochloa crus-galli -Echinodermata -Echinosciurus variegatoides -Echinosorex gymnura -Echinothrips americanus -Echyridella menziesii -Ecklonia maxima -Ecklonia radiata -Eclectus -Eclectus roratus -Eclipta -Eclipta alba -Eclipta prostrata -Ectobius sylvestris -Ectocarpus fasciculatus -Ectropis -Ectropis crepuscularia -Ectropis grisescens -Ectropis obliqua -Edgeworthia albiflora -Edgeworthia chrysantha -Edwardsiella -Edwardsiella anguillarum -Edwardsiella ictaluri -Edwardsiella piscicida -Edwardsiella tarda -Egaenus convexus -Eggerthella lenta -Egretta garzetta -Egretta picata -Ehrharta calycina -Ehrharta erecta -Eidolon dupreanum -Eidolon helvum -Eigenmannia virescens -Eimeria necatrix -Eimeria stiedai -Eisenia fetida -Elaeis guineensis -Elaphe dione -Elaphe taeniurus -Elaphodus cephalophus -Elaphurus davidianus -Elapsoidea loveridgei -Eleginus gracilis -Eleocharis dulcis -Elephantopus scaber -Elephas maximus -Elephas maximus indicus -Elettaria cardamomum -Eleusine coracana -Eleusine indica -Eleutheranthera ruderalis -Eleutheronema tetradactylum -Eliokarmos dubius -Elisabethiella stueckenbergi -Eliurus majori -Eliurus minor -Eliurus tanala -Elizabethkingia anophelis -Elliptio complanata -Elymus multisetus -Elymus repens -Emberiza chrysophrys -Emberiza cioides -Emberiza citrinella -Emberiza elegans -Emberiza pusilla -Emberiza rustica -Emberiza spodocephala -Emberiza tristrami -Embiratermes neotenicus -Embryophyta -Emilia sonchifolia -Emiliania huxleyi -Emiliania huxleyi CCMP373 -Emiliania huxleyi DWN 61/87/10 -Empidonax alnorum -Empidonax difficilis -Empidonax sp. -Empidonax traillii -Emys blandingii -Enantiopus melanogenys -Enchelyopus cimbrius -Encyclia -Endoconidiophora resinifera -Engraulis australis -Enhydra lutris -Enhydra lutris kenyoni -Enhydra lutris nereis -Enicognathus ferrugineus -Enneapterygius tutuilae -enrichment culture -Ensete superbum -Ensete ventricosum -Ensis minor -Entamoeba -Entamoeba gingivalis -Enterobacter -Enterobacter asburiae -Enterobacter cancerogenus -Enterobacter cloacae -Enterobacter cloacae complex -Enterobacter hormaechei -Enterobacter hormaechei subsp. xiangfangensis -Enterobacter kobei -Enterobacter ludwigii -Enterobacter sp. -Enterobacter sp. CT7 -Enterobacterales -Enterobacteriaceae -Enterobacteriaceae bacterium bta3-1 -Enterocloster bolteae -Enterococcus -Enterococcus faecalis -Enterococcus faecalis 62 -Enterococcus faecalis ATCC 19433 -Enterococcus faecalis ATCC 29212 -Enterococcus faecalis EF-01 -Enterococcus faecalis EnGen0211 -Enterococcus faecalis EnGen0243 -Enterococcus faecalis OG1RF -Enterococcus faecium -Enterococcus faecium E1071 -Enterococcus faecium TX1330 -Enterococcus gallinarum -Enterococcus hirae -Enterococcus sp. -Enterovibrio norvegicus -Entoleuca sp. -Entomophthora muscae -Eolophus roseicapilla -Eolophus roseicapillus x Cacatua sanguinea -Eonycteris spelaea -Eophona migratoria -Eopsaltria australis -Eos bornea -Eos reticulata -Eospalax rufescens -Eothenomys cachinus -Eothenomys chinensis -Eothenomys custos -Eothenomys eleusis -Eothenomys eva -Eothenomys inez -Eothenomys melanogaster -Eothenomys miletus -Eozapus setchuanus -Epalzeorhynchos frenatum -Epalzeorhynchos kalopterus -Epanerchodus kimi -Epichloe festucae -Epicoccum nigrum -Epidendrum -Epimedium -Epimedium pseudowushanense -Epinephelinae -Epinephelus -Epinephelus aeneus -Epinephelus akaara -Epinephelus areolatus -Epinephelus awoara -Epinephelus coioides -Epinephelus costae -Epinephelus fasciatus -Epinephelus fuscoguttatus -Epinephelus fuscoguttatus x Epinephelus lanceolatus -Epinephelus fuscoguttatus x Epinephelus polyphekadion -Epinephelus lanceolatus -Epinephelus malabaricus -Epinephelus marginatus -Epinephelus moara x Epinephelus lanceolatus -Epinephelus morio -Epinephelus quoyans -Epinephelus sp. -Epinephelus sp. C AA-2018 -Epinephelus sp. D AA-2018 -Epinephelus sp. E AA-2018 -Epinephelus sp. F AA-2018 -Epinephelus sp. G AA-2018 -Epinephelus sp. H AA-2018 -Epinephelus sp. I AA-2018 -Epinephelus tauvina -Epinotia aporema -Epipogium roseum -Epipomponia nawai -Epipremnum aureum -Epiprocta -Epirrita autumnata -Episoriculus leucops -Episyrphus balteatus -Epomophorus -Epomophorus gambianus -Epomophorus labiatus -Epomophorus pusillus -Epomophorus wahlbergi -Epomops -Epomops buettikoferi -Epomops franqueti -Epomops sp. -Eptatretus burgeri -Eptesicus -Eptesicus brasiliensis -Eptesicus diminutus -Eptesicus furinalis -Eptesicus fuscus -Eptesicus hottentotus -Eptesicus isabellinus -Eptesicus japonensis -Eptesicus nilssonii -Eptesicus regulus -Eptesicus serotinus -Eptesicus serotinus andersoni -Eptesicus serotinus serotinus -Eptesicus sp. -Equidae -Equus -Equus asinus -Equus asinus africanus -Equus asinus asinus -Equus asinus somalicus -Equus asinus x Equus caballus -Equus caballus -Equus caballus x Equus asinus -Equus ferus -Equus grevyi -Equus hemionus -Equus hemionus onager -Equus kiang -Equus przewalskii -Equus quagga -Equus quagga burchellii -Equus sp. -Equus zebra zebra -Eragrostideae -Eragrostis -Eragrostis curvula -Eragrostis minor -Erannis ankeraria -Erannis defoliaria -Eratigena atrica -Erechtites valerianifolius -Erethizon dorsatum -Eretmapodites -Eretmapodites chrysogaster -Eretmapodites leucopous -Eretmapodites quinquevittatus -Eretmapodites silvestris -Eretmochelys imbricata -Eretmodus cyanostictus -Erigeron -Erigeron annuus -Erigeron breviscapus -Erigeron canadensis -Erinaceinae -Erinaceus -Erinaceus amurensis -Erinaceus europaeus -Erinaceus roumanicus -Erinaceus sp. -Erinnyis ello -Eriocheir sinensis -Eriochilus dilatatus -Eriochloa polystachya -Eristalis arbustorum -Eristalis pertinax -Eristalis tenax -Erithacus rubecula -Erodium -Erodium ciconium -Erodium cicutarium -Erthesina fullo -Eruca vesicaria -Eruca vesicaria subsp. sativa -Erwinia -Erwinia amylovora -Erwinia billingiae -Erwinia horticola -Erwinia iniecta -Erwinia persicina -Erwinia pyrifoliae -Erwinia rhapontici -Erwinia sp. -Erwinia tracheiphila -Eryngium -Erysimum -Erysimum cheiri -Erysimum linifolium -Erysipelothrix rhusiopathiae -Erysiphe necator -Erysiphe palczewskii -Erysiphe sp. -Erysiphe trifoliorum -Erythemis simplicicollis -Erythrina -Erythrina crista-galli -Erythrobacter litoralis -Erythrobacter sp. -Erythrocebus patas -Erythrodiplax fusca -Erythrodiplax umbrata -Erythrura prasina -Escherichia -Escherichia coli -Escherichia coli 55989 -Escherichia coli APEC O78 -Escherichia coli ATCC 25922 -Escherichia coli B -Escherichia coli BL21 -Escherichia coli BL21(DE3) -Escherichia coli BW25113 -Escherichia coli C -Escherichia coli CFT073 -Escherichia coli DH5[alpha] -Escherichia coli H21 -Escherichia coli H8 -Escherichia coli IHE3034 -Escherichia coli J53 -Escherichia coli K-12 -Escherichia coli K1 -Escherichia coli LF82 -Escherichia coli MC1061 -Escherichia coli MP1 -Escherichia coli NC101 -Escherichia coli O103 -Escherichia coli O103:H11 -Escherichia coli O103:H25 str. NIPH-11060424 -Escherichia coli O104:H4 -Escherichia coli O111:H2 -Escherichia coli O113:H4 -Escherichia coli O127:B8 -Escherichia coli O145 -Escherichia coli O145:NM -Escherichia coli O153 -Escherichia coli O156:H25 -Escherichia coli O157 -Escherichia coli O157:H43 str. T22 -Escherichia coli O157:H7 -Escherichia coli O157:H7 str. EDL933 -Escherichia coli O177 -Escherichia coli O18 -Escherichia coli O26:H11 -Escherichia coli O78 -Escherichia coli O8:H19 -Escherichia coli PA11 -Escherichia coli PA2 -Escherichia coli PA28 -Escherichia coli PA32 -Escherichia coli PA33 -Escherichia coli PA4 -Escherichia coli PA42 -Escherichia coli PA45 -Escherichia coli PA5 -Escherichia coli PA8 -Escherichia coli RS218 -Escherichia coli str. K-12 substr. DH10B -Escherichia coli str. K-12 substr. MG1655 -Escherichia coli str. K-12 substr. W3110 -Escherichia coli W -Escherichia fergusonii -Escherichia sp. -Escherichia sp. MOD1-EC6098 -Escobaria missouriensis -Esocidae -Esox lucius -Esox masquinongy -Estrilda melpoda -Estrilda troglodytes -Etheostoma fonticola -Etroplus canarensis -Etroplus suratensis -Eubalaena australis -Eubleekeria splendens -Eucalanus bungii -Eucalyptus urophylla -Eucampsipoda africana -Eucampsipoda sundaica -Eucera clypeata -Eucera eucnemidea -Eucera nigrescens -Eucera nigrifacies -Eucera pruinosa -Eucera sp. -Euchaeta -Eucharis adscendens -Eucharis x grandiflora -Eucnemidae sp. -Eucomis -Eucomis punctata -Eucommia ulmoides -Euderma maculatum -Eudiplozoon nipponicum -Eudocimus -Eudocimus albus -Eudorcas thomsonii -Eudromia elegans -Eudyptes chrysocome -Eudyptula minor -Eulemur coronatus -Eulemur macaco -Eulemur rufifrons -Eulipotyphla -Eumantispa harmandi -Eumeces schneideri -Eumenes papillarius -Eumetopias jubatus -Eumetopina flavipes -Eumops auripendulus -Eumops bonariensis -Eumops glaucinus -Eumops patagonicus -Eumops perotis -Eunectes murinus -Eunicea flexuosa -Eunymphicus cornutus -Euonymus alatus -Euonymus maackii -Eupatorium -Eupatorium glehni -Eupatorium makinoi -Eupelmus vesicularis -Euphagus cyanocephalus -Euphausia pacifica -Euphausia superba -Euphorbia -Euphorbia caput-medusae -Euphorbia helioscopia -Euphorbia heterophylla -Euphorbia hirta -Euphorbia hypogaea -Euphorbia marginata -Euphorbia milii -Euphorbia milii var. splendens -Euphorbia peplus -Euphorbia pulcherrima -Euphorbia tithymaloides -Euplectes afer -Euplexia lucipara -Eupodotis senegalensis -Euprepiophis mandarinus -Eupristina koningsbergeri -Euproctis chrysorrhoea -Euproctis pseudoconspersa -Euproctis similis -Eupsittula aurea -Eurema hecabe -Eurillas virens -Eurycea wilderae -Eurysacca quinoae -Euscelidius variegatus -Euscorpius sicanus -Eustachys petraea -Eustoma -Eustoma grandiflorum -Eustrephus latifolius -Eutrema japonicum -Eutrigla gurnardus -Euvarroa sinhai -Euxoa ochrogaster -Evansella clarkii -Evasterias troschelii -Eviota zebrina -Evynnis cardinalis -Evynnis tumifrons -Exiguobacterium alkaliphilum -Exiguobacterium aurantiacum -Exitianus capicola -Exitianus exitiosus -Exobasidium gracile -Exomis microphylla -Exoneura -Exserohilum turcicum -Exyrias -Eysarcoris guttigerus -Fabaceae -Faecalibacterium prausnitzii -Fagopyrum esculentum -Fagus sylvatica -Falcatifolium taxoides -Falco -Falco cherrug -Falco columbarius -Falco fasciinucha -Falco femoralis septentrionalis -Falco mexicanus -Falco naumanni -Falco peregrinus -Falco peregrinus nesiotes -Falco punctatus -Falco rusticolus -Falco rusticolus x Falco peregrinus -Falco sparverius -Falco subbuteo -Falco tinnunculus -Falco vespertinus -Falcunculus frontatus -Fallopia convolvulus -Fallopia dumetorum -Fallopia multiflora -Falsistrellus mackenziei -Fannia -Farfugium japonicum -Fasciola gigantica -Fasciola hepatica -Fatsia japonica -Fejervarya limnocharis -Feldmannia -Felidae -Feliformia -Felis -Felis catus -Felis nigripes -Felis silvestris -Felis silvestris lybica -Felis sp. -Ferdinandea cuprea -Ferocactus cylindraceus -Ferula assa-foetida -Festuca -Festuca ambigua -Festuca californica -Festuca contracta -Festuca myuros -Festuca novaezealandiae -Festuca ovina -Festuca pratensis -Festuca rubra -Fevillea cordifolia -Fevillea trilobata -Ficedula mugimaki -Ficedula parva -Ficedula zanthopygia -Ficus -Ficus carica -Ficus elastica -Ficus heterophylla -Ficus microcarpa -Ficus palmata -Ficus virens -Ficus virgata -Fimbristylis littoralis -Flammulina velutipes -Flavobacterium -Flavobacterium columnare -Flavobacterium columnare NBRC 100251 = ATCC 23463 -Flavobacterium psychrophilum -Flavobacterium sp. -Flavobacterium sp. B183 -Flavobacterium sp. LMO6 -Flavobacterium sp. LMO8 -Flavobacterium sp. LMO9 -Florenciella -Fomitiporia mediterranea -Fontinalis antipyretica -Forcipomyia taiwana -Forficula auricularia -Formica aquilonia -Formica aserva -Formica cinerea -Formica exsecta -Formica fusca -Formica pressilabris -Formica truncorum -Formicarius analis -Formicidae -Forpus coelestis -Forpus xanthopterygius -Forsythia mandschurica -Forsythia suspensa -Fragaria -Fragaria chiloensis -Fragaria vesca -Fragaria x ananassa -Francolinus pintadeanus -Frankliniella intonsa -Frankliniella occidentalis -Frankliniella schultzei -Frankliniella zucchini -Fratercula arctica -Fratercula corniculata -Fraxinus americana -Fraxinus chinensis -Fraxinus chinensis subsp. rhynchophylla -Fraxinus excelsa -Fraxinus excelsior -Fraxinus ornus -Fraxinus sp. -Freesia -Freesia hybrid cultivar -Freesia refracta -Fregata magnificens -Fringilla coelebs -Fringilla montifringilla -Fringillidae -Frisvollia varia -Fritillaria imperialis -Fritillaria thunbergii -Fuchsia -Fucus serratus -Fulgoroidea -Fulica -Fulica americana -Fulica armillata -Fulica atra -Fulica rufifrons -Fulmarus glacialis -Fumaria officinalis -Fundulus heteroclitus -Fundulus heteroclitus heteroclitus -Fungi -Funisciurus -Funisciurus anerythrus -Funisciurus bayonii -Furcifer pardalis -Furcraea -Fusarium andiyazi -Fusarium asiaticum -Fusarium boothii -Fusarium bullatum -Fusarium cerealis -Fusarium circinatum -Fusarium coeruleum -Fusarium concentricum -Fusarium culmorum -Fusarium equiseti -Fusarium globosum -Fusarium graminearum -Fusarium incarnatum -Fusarium langsethiae -Fusarium mangiferae -Fusarium nygamai -Fusarium oxysporum -Fusarium oxysporum f. sp. dianthi -Fusarium oxysporum f. sp. melonis -Fusarium poae -Fusarium proliferatum -Fusarium pseudograminearum -Fusarium redolens -Fusarium sacchari -Fusarium sambucinum -Fusarium solani -Fusarium sp. -Fusarium subglutinans -Fusarium vanettenii -Fusarium verticillioides -Fusarium virguliforme -Fusobacterium nucleatum -Gadiculus argenteus -Gadidae -Gadus -Gadus chalcogrammus -Gadus macrocephalus -Gadus morhua -Gaeumannomyces graminis -Gaeumannomyces tritici -Gaidropsarus mediterraneus -Gaillardia -Gaillardia aristata -Gaillardia x grandiflora -Galago senegalensis -Galanthus -Galaxias maculatus -Galeocerdo cuvier -Galerella pulverulenta -Galerella sanguinea -Galeus sauteri -Galictis cuja -Galidia elegans -Galinsoga parviflora -Galinsoga quadriradiata -Galium aparine -Galium mexicanum -Galium odoratum -Galleria mellonella -Gallicrex cinerea -Galliformes -Gallinago gallinago -Gallinula -Gallinula chloropus -Gallus -Gallus gallus -Gallus gallus gallus -Gallus sonneratii -Gallus sp. -Galphimia -Galtonia -Gambierdiscus carpenteri -Gambusia holbrooki -Gammaproteobacteria -Gammaproteobacteria bacterium -Gammarus chevreuxi -Gammarus pulex -Gammarus sp. -Gamochaeta pensylvanica -Gardenia jasminoides -Gardnerella vaginalis -Gardnerycteris crenulatum -Garra rufa -Garrulax canorus -Garrulus glandarius -Gasteracantha cancriformis -Gasterosteus aculeatus -Gastropoda -Gavia immer -Gazania -Gazella -Gazella arabica -Gazella bennettii -Gazella dorcas -Gazella gazella -Gazella spekei -Gazella subgutturosa -Gazella subgutturosa marica -Gazza minuta -Gehyra lauta -Gekko gecko -Gekko similignum -Gemmamyces piceae -Gemmata -Genetta -Genetta genetta -Gentiana -Gentiana macrophylla -Gentiana scabra -Gentiana scabra x Gentiana triflora -Gentiana sp. -Gentiana triflora -Geobacillus -Geobacillus kaustophilus -Geobacillus sp. 6k51 -Geobacillus stearothermophilus -Geobacillus thermodenitrificans -Geobacter sp. -Geoclemys hamiltonii -Geodorum -Geopelia humeralis -Geopelia placida -Geophagus brasiliensis -Geopora sumneriana -Geospiza -Geospiza fortis -Geospiza fuliginosa -Geothlypis tolmiei -Geothlypis trichas -Geotria australis -Geotrichum candidum -Geotrygon montana -Gephyroberyx darwinii -Geranium -Geranium carolinianum -Geranium dissectum -Geranium pusillum -Geranium robertianum -Geranium rotundifolium -Geranium sp. -Geranium thunbergii -Gerbera -Gerbera hybrid cultivar -Gerbera jamesonii -Gerbillinae -Gerbilliscus kempi -Gerbilliscus leucogaster -Gerbilliscus sp. -Gerrhosaurus nigrolineatus -Gerridae -Gerridae sp. -Gerygone albofrontata -Gevuina avellana -Giardia -Giardia intestinalis -Giardia intestinalis assemblage E -Gigantidas vrijenhoeki -Gigantochloa levis -Gigaspora margarita -Gigaspora rosea -Gilliamella apicola -Gilpinia hercyniae -Ginkgo biloba -Giraffa camelopardalis -Giraffa giraffa -Giraffa reticulata -Girardia dorotocephala -Girardia tigrina -Girella tricuspidata -Gladiolus -Gladiolus dalenii -Gladiolus hybrid cultivar -Glaesserella parasuis -Glandularia canadensis -Glandularia pulchella -Glandularia x hybrida -Glaresis -Glauconycteris -Glauconycteris poensis -Glauconycteris variegata -Glebionis coronaria -Glebionis segetum -Glehnia littoralis -Gliridae -Glis glis -Globicephala macrorhynchus -Globicephala melas -Globisporangium nunn -Globisporangium polare -Globisporangium splendens -Globisporangium ultimum -Globodera pallida -Globodera rostochiensis -Glomeridella minima -Gloriosa -Gloriosa superba -Glossina morsitans morsitans -Glossina pallidipes -Glossophaga commissarisi -Glossophaga soricina -Glossophaginae -Glossopsitta concinna -Gloxinia -Gloydius angusticeps -Gluconobacter cerinus -Glutamicibacter arilaitensis -Glutamicibacter halophytocola -Glycaspis brimblecombei -Glyceria elata -Glyceria striata -Glycine clandestina -Glycine max -Glycine soja -Glycosmis pentaphylla -Glycyrrhiza glabra -Glyphodes pulverulentalis -Glyphorynchus spirurus -Glypta fumiferanae -Glyptapanteles flavicoxis -Glyptapanteles indiensis -Glyptemys insculpta -Glyptemys muhlenbergii -Glyptostrobus pensilis -Gobiidae sp. -Gobio gobio -Gobiomorphus cotidianus -Gobius sp. -Golovinomyces cichoracearum -Gomesa bifolia -Gomphocarpus physocarpus -Gompholobium preissii -Gomphostemma niveum -Gomphrena globosa -Gongronemopsis latifolia -Gongylopus adiposus -Gonimbrasia cytherea -Goniolimon tataricum -Goniopsis cruentata -Gonipterus platensis -Goniurosaurus luii -Gonolabis marginalis -Gonorynchus abbreviatus -Gonyosoma oxycephalum -Gopherus -Gopherus agassizii -Gopherus berlandieri -Gordonia -Gordonia alkanivorans -Gordonia malaquae -Gordonia neofelifaecis -Gordonia rubripertincta -Gordonia sp. (in: high G+C Gram-positive bacteria) -Gordonia sputi -Gordonia terrae -Gordonia westfalica -Gorilla -Gorilla beringei beringei -Gorilla beringei graueri -Gorilla gorilla -Gorilla gorilla diehli -Gorilla gorilla gorilla -Gorytes laticinctus -Gossypium -Gossypium arboreum -Gossypium barbadense -Gossypium darwinii -Gossypium davidsonii -Gossypium gossypioides -Gossypium harknessii -Gossypium herbaceum -Gossypium hirsutum -Gossypium hirsutum subsp. latifolium -Gossypium hirsutum var. punctatum -Gossypium lobatum -Gossypium mustelinum -Gossypium raimondii -Gossypium somalense -Gossypium stocksii -Gossypium thurberi -Gossypium tomentosum -Goura cristata -Goura scheepmakeri -Gracilaria vermiculophylla -Gracula religiosa -Grallina cyanoleuca -Graminella nigrifrons -Grammomys macmillani -Grammomys sp. -Grammomys surdaster -Grampus griseus -Graphiurus murinus -Graphocephala fennahi -Grapholita funebrana -Grapholitha molesta -Graptemys geographica -Graptopetalum paraguayense -Gremmeniella abietina -Grifola frondosa -Griselinia lucida -Grosmannia clavigera -Gruidae -Grus americana -Grus grus -Grus japonensis -Grus monacha -Grus nigricollis -Grus paradisea -Grus virgo -Gryllidae -Grylloblatta bifratrilecta -Gryllodes sigillatus -Gryllotalpa orientalis -Gryllus assimilis -Guaruba guarouba -Gubernatrix cristata -Guinardia delicatula -Guira guira -Guizotia abyssinica -Gulo gulo -Gymnadenia conopsea -Gymnadenia rhellicani -Gymnadenia x densiflora -Gymnanthemum amygdalinum -Gymnema sylvestre -Gymnocalycium mihanovichii -Gymnocladus dioicus -Gymnocorymbus ternetzi -Gymnocypris namensis -Gymnogyps californianus -Gymnopithys rufigula -Gymnorhina tibicen -Gymnosporia buxifolia -Gymnothorax reticularis -Gynandropsis gynandra -Gynochthodes officinalis -Gynostemma pentaphyllum -Gynura aurantiaca -Gynura japonica -Gynura procumbens -Gyps fulvus -Gyps himalayensis -Gyps indicus -Gypsophila -Gypsophila elegans -Gypsophila paniculata -Gyrinophilus porphyriticus -Gyromitra esculenta -Habenaria radiata -Haemadipsa -Haemadipsa picta -Haemadipsa zeylanica -Haemagogus -Haemagogus equinus -Haemagogus janthinomys -Haemagogus leucocelaenus -Haemagogus lucifer -Haemagogus spegazzinii -Haemanthus albiflos -Haemaphysalis -Haemaphysalis bancrofti -Haemaphysalis campanulata -Haemaphysalis concinna -Haemaphysalis doenitzi -Haemaphysalis flava -Haemaphysalis formosensis -Haemaphysalis hystricis -Haemaphysalis intermedia -Haemaphysalis japonica -Haemaphysalis leporispalustris -Haemaphysalis longicornis -Haemaphysalis megaspinosa -Haemaphysalis montgomeryi -Haemaphysalis papuana -Haemaphysalis parva -Haemaphysalis punctata -Haemaphysalis qinghaiensis -Haemaphysalis sp. -Haemaphysalis spinigera -Haemaphysalis sulcata -Haemaphysalis turturis -Haemaphysalis yeni -Haematobia irritans -Haematopus ater -Haematopus moquini -Haematopus ostralegus -Haematopus palliatus -Haematopus unicolor -Haemophilus -Haemophilus influenzae -Haemorhous mexicanus -Hafnia alvei -Hafnia paralvei -Hafnia sp. -Halcyon smyrnensis -Haliaeetus albicilla -Haliaeetus leucocephalus -Haliaeetus leucogaster -Haliaeetus pelagicus -Halichoeres marginatus -Halichoeres melanurus -Halichoerus grypus -Halichondria panicea -Halictidae sp. -Halictus cochlearitarsis -Halictus flavipes -Halictus fulvipes -Halictus rubicundus -Halictus scabiosae -Halictus simplex -Halictus sp. -Halictus sp. EUR01 -Halictus tectus -Halieutaea stellata -Haliotis discus -Haliotis discus discus -Haliotis discus hannai -Haliotis diversicolor -Haliotis diversicolor aquatilis -Haliotis madaka -Haliplus fluviatilis -Halisarca dujardinii -Haloarcula californiae -Haloarcula hispanica -Haloarcula hispanica ATCC 33960 -Haloarcula japonica -Haloarcula sinaiiensis -Haloarcula vallismortis -Halobacterium -Halobacterium salinarum -Halobacterium salinarum R1 -Halobatrachus didactylus -Halocarpus bidwillii -Halocynthia -Halocynthia roretzi -Haloferax -Haloferax gibbonsii -Haloferax volcanii -Halogeometricum sp. CG-9 -Halogranum sp. SS5-1 -Halomonas -Halomonas aquamarina -Halomonas meridiana -Halomonas sp. -Halomonas ventosae -Halophytophthora -Haloquadratum -Halorubrum -Halorubrum coriense -Halorubrum lacusprofundi -Halorubrum sodomense -Halorubrum sp. -Halorubrum sp. B2-2 -Halorubrum sp. LN27 -Halorubrum sp. PV6 -Halorubrum sp. s5a-3 -Halorubrum sp. SP3-3 -Halorubrum sp. SS5-4 -Halorubrum sp. SS7-4 -Halyomorpha halys -Hanseniella sp. AD-2014 -Hapalemur griseus -Haplochromis burtoni -Haplopappus -Haptolina ericina -Haptolina hirta -Hardenbergia comptoniana -Hardenbergia violacea -Harmonia axyridis -Harrisina brillians -Haslea ostrearia -Hebeloma mesophaeum -Hebius popei -Hedera helix -Hedyotis uncinella -Heimyscus fumosus -Helarctos malayanus -Helenium -Helianthus -Helianthus annuus -Helianthus niveus -Helice tientsinensis -Helichrysum -Helichrysum revolutum -Helichrysum stoechas -Helicobacter pylori -Helicobacter pylori B45 -Helicobasidium mompa -Helicolenus barathri -Heliconia -Heliconius erato -Helicoverpa -Helicoverpa armigera -Helicoverpa assulta -Helicoverpa gelotopoeon -Helicoverpa zea -Heliocidaris crassispina -Heliosciurus gambianus -Heliothis -Heliothis peltigera -Heliothis subflexa -Heliothis virescens -Heliotropium europaeum -Heliotropium lasiocarpum -Heliotropium szovitsii -Helleborus -Helleborus niger -Helleborus x hybridus -Helminthotheca echioides -Heloderma horridum -Heloderma suspectum -Helpis minitabunda -Hemerobius handschini -Hemerobius nitidulus -Hemerocallis -Hemerocallis fulva -Hemibagrus guttatus -Hemiculter leucisculus -Hemidactylus bowringii -Hemidactylus frenatus -Hemidesmus indicus -Hemigrapsus takanoi -Hemileuca -Hemiphaga novaeseelandiae -Hemiphlebia mirabilis -Hemitheconyx caudicinctus -Hemitragus jemlahicus -Hemitriakis japanica -Hemitrygon akajei -Henricia sp. AR-2014 -Hepatica -Heracleum moellendorffii -Heracleum sphondylium -Heriades crenulata -Heriades rubicola -Heriades truncorum -Herissantia -Herissantia crispa -Hermannia gibba -Hermannia sp. (in: mites & ticks) -Herniaria -Herpestes ichneumon -Herpestes urva -Herpestidae -Hesperosciurus griseus -Heterixalus madagascariensis -Heterobasidion abietinum -Heterobasidion annosum -Heterobasidion australe -Heterobasidion ecrustosum -Heterobasidion irregulare -Heterobasidion occidentale -Heterobasidion parviporum -Heterocaecilius solocipennis -Heterodera glycines -Heterodera schachtii -Heterodontonyx -Heteromys -Heteromys pictus -Heteronetta atricapilla -Heteropelma amictum -Heteropsilopus ingenuus -Heteroptera -Heterosigma akashiwo -Heterosiphonia pulchra -Heterotermes ferox -Hevea brasiliensis -Hewittia sublobata -Hexapoda -Hexura picea -Hibbertia scandens -Hibiscus -Hibiscus arnottianus -Hibiscus cannabinus -Hibiscus rosa-sinensis -Hibiscus sabdariffa -Hibiscus sp. -Hibiscus syriacus -Hieraaetus pennatus -Hieracium -Himantopus himantopus -Himantopus melanurus -Himantopus mexicanus -Himatione sanguinea -Hime japonica -Hippeastrum -Hippeastrum hybrid cultivar -Hippeastrum sp. -Hippobosca equina -Hippoboscidae -Hippoboscoidea -Hippocamelus bisulcus -Hippocampus erectus -Hippoglossus -Hippoglossus hippoglossus -Hippophae rhamnoides -Hippopotamus -Hippopotamus amphibius -Hipposideridae -Hipposideros -Hipposideros abae -Hipposideros armiger -Hipposideros beatus -Hipposideros bicolor -Hipposideros caffer -Hipposideros cervinus -Hipposideros cf. ruber -Hipposideros cineraceus -Hipposideros curtus -Hipposideros diadema -Hipposideros fuliginosus -Hipposideros galeritus -Hipposideros grandis -Hipposideros larvatus -Hipposideros lekaguli -Hipposideros pomona -Hipposideros pratti -Hipposideros ruber -Hipposideros terasensis -Hipposideros turpis -Hippotragus equinus -Hippotragus niger -Hirschfeldia incana -Hirundinidae -Hirundo rustica -Histiostoma -Histiotus laephotis -Histiotus macrotus -Histiotus montanus -Histiotus sp. -Histiotus velatus -Histrionicus histrionicus -Holcus lanatus -Holochilus chacarius -Holochilus sciureus -Hologymnosus -Holothuria atra -Holothuria sinica -Holothuroidea -Homalodisca vitripennis -Homalopsis buccata -Homarus gammarus -Homo -Homo sapiens -Homona coffearia -Homona magnanima -Hoolock hoolock -Hoplichthys -Hoplitis adunca -Hoplobatrachus occipitalis -Hoplobatrachus rugulosus -Hoplobatrachus tigerinus -Hoplodrina ambigua -Horabagrus nigricollaris -Hordeum bulbosum -Hordeum jubatum -Hordeum murinum -Hordeum sp. -Hordeum vulgare -Hordeum vulgare subsp. spontaneum -Hordeum vulgare subsp. vulgare -Hordeum vulgare var. hexastichon -Hortaea werneckii -Hospitalitermes bicolor -Hosta -Hosta fortunei -Hosta longipes -Hosta minor -Hosta sieboldii -Houttuynia cordata -Hovenia dulcis -Hoya -Hoya arnottiana -Hoya australis -Hoya calycina -Hoya carnosa -Hoya lambii -Hoya wayetii -Hsunycteris thomasi -Hucho taimen -human metagenome -Humulus -Humulus japonicus -Humulus lupulus -Humulus lupulus var. cordifolius -Hungatella -Huso huso -Hyacinthus -Hyacinthus orientalis -Hyaena hyaena -Hyaenidae -Hyalomma -Hyalomma aegyptium -Hyalomma anatolicum -Hyalomma anatolicum anatolicum -Hyalomma asiaticum -Hyalomma asiaticum asiaticum -Hyalomma detritum -Hyalomma dromedarii -Hyalomma excavatum -Hyalomma impeltatum -Hyalomma isaaci -Hyalomma lusitanicum -Hyalomma marginatum -Hyalomma marginatum marginatum -Hyalomma plumbeum -Hyalomma plumbeum plumbeum -Hyalomma rufipes -Hyalomma scupense -Hyalomma sp. -Hyalomma truncatum -Hyalopterus pruni -Hyblaea puera -Hybognathus hankinsoni -Hybomys -Hybomys univittatus -hybrid -Hydra oligactis -Hydra vulgaris -Hydrangea -Hydrangea febrifuga -Hydrangea macrophylla -Hydrellia griseola -Hydrocharis dubia -Hydrochoerus hydrochaeris -Hydrocoloeus minutus -Hydrocotyle umbellata -Hydrocotyle verticillata -Hydrocotyle vulgaris -Hydrogenobaculum -Hydrogenophilus thermoluteolus -Hydropotes inermis -Hydroprogne caspia -Hygrophorus penarioides -Hyla simplex -Hylaeamys megacephalus -Hylaeamys yunganus -Hylaeus angustatus -Hylaeus gibbus -Hylaeus punctatus -Hylaeus sp. -Hylobates agilis -Hylobates albibarbis -Hylobates lar -Hylobates moloch -Hylobates muelleri -Hylobates pileatus -Hylobates sp. -Hylobatidae -Hylocereus -Hylocichla mustelina -Hylomyscus -Hylomyscus endorobae -Hylomyscus pamfi -Hylomyscus parvus -Hylomyscus simus -Hylomyscus stella -Hylopetes -Hylopetes phayrei -Hymenocallis -Hymenocallis littoralis -Hymenoscyphus albidus -Hymenoscyphus fraxineus -Hynobius nebulosus -Hyoscyamus muticus -Hyparrhenia hirta -Hypena scabra -Hypera postica -Hypericum japonicum -Hypericum perforatum -Hyphantria cunea -Hyphessobrycon -Hypochaeris -Hypochaeris chillensis -Hypochaeris radiata -Hypochaeris radicata -Hypocnemis cantator -Hypolimnas bolina -Hypomyces chrysospermus -Hypophthalmichthys molitrix -Hypophthalmichthys nobilis -Hyporhamphus australis -Hyporhamphus sajori -Hyporthodus septemfasciatus -Hyposidra infixaria -Hyposidra talaca -Hyposoter -Hyposoter didymator -Hyposoter fugitivus -Hypothymis azurea -Hypseleotris klunzingeri -Hypsignathus monstrosus -Hypsipetes amaurotis -Hypsizygus marmoreus -Hypsugo -Hypsugo alaschanicus -Hypsugo pulveratus -Hypsugo savii -Hyptiotes gertschi -Hystricidae -Hystricomorpha -Hystrix brachyura -Hystrix cristata -Ia io -Iberis semperflorens -Iberolacerta cyreni -Iberolacerta monticola -Ibicella lutea -Ichneumia albicauda -Ichthyaetus ichthyaetus -Ichthyaetus leucophthalmus -Ichthyaetus melanocephalus -Ichthyophis bannanicus -Ichthyophonus hoferi -Ichthyosaura alpestris -Ichthyosaura alpestris cyreni -Ichthyscopus lebeck -Ictalurus furcatus -Ictalurus punctatus -Icteria virens -Icterus spurius -Ictinia mississippiensis -Idaea seriata -Idiomarinaceae -Idiomarinaceae bacterium M2-2 -Idiomarinaceae bacterium N2-2 -Idiophlebotomus -Idotea -Iguana iguana -Iguania -Ilex cornuta -Ilex paraguariensis -Illicium anisatum -Ilyonectria crassa -Ilyonectria destructans -Ilyonectria pseudodestructans -Ilyonectria robusta -Impatiens -Impatiens balsamina -Impatiens hawkeri -Impatiens walleriana -Imperata cylindrica -Indomegoura indica -Indopacetus pacificus -Indotestudo elongata -Indotestudo forstenii -Indri indri -Inia boliviensis -Inimicus japonicus -Inopus -Inopus flavus -Insecta -Insecta sp. -Inula japonica -Iodobacter sp. CdM7 -Ipomoea -Ipomoea alba -Ipomoea aquatica -Ipomoea batatas -Ipomoea cairica -Ipomoea hederifolia -Ipomoea indica -Ipomoea microdactyla -Ipomoea nil -Ipomoea obscura -Ipomoea owariensis -Ipomoea purpurea -Ipomoea repens -Ipomoea rubens -Ipomoea setosa -Ipomoea sinensis -Ipomoea spathulata -Ipomoea stenobasis -Ipomoea tenuirostris -Ipomoea triloba -Ipomoea wightii -Ips typographus -Iragoides fasciata -Iresine herbstii -Iris -Iris albicans -Iris domestica -Iris ensata -Iris germanica -Iris japonica -Iris tectorum -Iris tingitana -Iris versicolor -Iris x hollandica -Iris xiphium -Isatis tinctoria -Ischnopsyllidae -Ischnoptera deropeltiformis -Ischnura posita -Ischnura ramburii -Ischnura senegalensis -Ishige okamurae -Isleria hauxwelli -Ismene -Isochrysis -Isoetes lacustris -Isognathotermes ugandensis -Isoodon macrourus -Isoodon obesulus -Isopoda -Istigobius decoratus -Istigobius goldmanni -Istigobius nigroocellatus -Istigobius ornatus -Istigobius rigilius -Ixeridium dentatum -Ixeris chinensis -Ixias marianne -Ixobrychus eurhythmus -Ixobrychus minutus -Ixobrychus sinensis -Ixodes -Ixodes acutitarsus -Ixodes canisuga -Ixodes cookei -Ixodes crenulatus -Ixodes dentatus -Ixodes eudyptidis -Ixodes frontalis -Ixodes granulatus -Ixodes hexagonus -Ixodes holocyclus -Ixodes lividus -Ixodes marxi -Ixodes nipponensis -Ixodes ovatus -Ixodes pavlovskyi -Ixodes persulcatus -Ixodes putus -Ixodes redikorzevi -Ixodes ricinus -Ixodes scapularis -Ixodes signatus -Ixodes simplex -Ixodes sinensis -Ixodes sp. -Ixodes trichosuri -Ixodes turdus -Ixodes uriae -Ixodes vespertilionis -Ixodida -Ixodida sp. -Ixodidae -Ixodoidea -Ixora coccinea -Jacquemontia -Jacquemontia pentanthos -Jacquemontia tamnifolia -Janthinobacterium lividum -Jasminum -Jasminum laurifolium f. nitidum -Jasminum multiflorum -Jasminum officinale -Jasminum sambac -Jatropha -Jatropha curcas -Jatropha gossypiifolia -Jatropha integerrima -Jatropha multifida -Jatropha podagrica -Javesella pellucida -Johnius dussumieri -Juglandaceae -Juglans -Juglans microcarpa -Juglans regia -Juglans sp. -Julidochromis dickfeldi -Julidochromis ornatus -Juliomys -Junco hyemalis -Junco hyemalis hyemalis -Juncus -Juncus compressus -Juncus maritimus -Juncus torreyi -Junonia coenia -Junonia lemonias -Justicia adhatoda -Justicia procumbens -Jynx torquilla -Kalanchoe -Kalanchoe blossfeldiana -Kalanchoe marnieriana -Kalanchoe tomentosa -Kaloula pulchra -Kappaphycus alvarezii -Kareius bicoloratus -Karelinia caspia -Katsuwonus pelamis -Kennedia prostrata -Kennedia rubicunda -Kerivoula argentata -Kerivoula hardwickii -Kerivoula pellucida -Kerivoula titania -Kerria lacca -Kinosternon subrubrum -Kitagawia praeruptora -Kitasatospora aureofaciens -Klebsiella -Klebsiella aerogenes -Klebsiella michiganensis -Klebsiella oxytoca -Klebsiella pneumoniae -Klebsiella pneumoniae ATCC 43816 -Klebsiella pneumoniae KCTC 2242 -Klebsiella pneumoniae subsp. pneumoniae KKBO-1 -Klebsiella pneumoniae subsp. pneumoniae KPNIH1 -Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 -Klebsiella quasipneumoniae -Klebsiella sp. -Klebsiella sp. 390 -Klebsiella variicola -Klebsiella variicola subsp. variicola -Kluyvera -Kluyvera cryocrescens -Kobus ellipsiprymnus -Koeleria macrantha -Kogia breviceps -Kogia sima -Komagataeibacter xylinus -Kosakonia cowanii -Kraftionema allantoideum -Kryptopterus bicirrhis -Kuhlia rupestris -Kummerowia striata -Kurthia gibsonii -Labeo catla -Labeo rohita -Labidiaster annulatus -Labidocera aestiva -Labiotermes -Lablab purpureus -Labroides dimidiatus -Labrus bergylta -Lacanobia oleracea -Lacerta agilis agilis -Lacerta schreiberi -Lachenalia -Lachenalia aloides -Lactarius rufus -Lactarius tabidus -Lacticaseibacillus casei -Lacticaseibacillus casei BL23 -Lacticaseibacillus casei W56 -Lacticaseibacillus paracasei -Lacticaseibacillus rhamnosus -Lactiplantibacillus pentosus -Lactiplantibacillus plantarum -Lactobacillus -Lactobacillus apis -Lactobacillus crispatus -Lactobacillus delbrueckii -Lactobacillus delbrueckii subsp. bulgaricus -Lactobacillus delbrueckii subsp. lactis -Lactobacillus gasseri -Lactobacillus gasseri ADH -Lactobacillus helveticus -Lactobacillus jensenii -Lactobacillus johnsonii -Lactobacillus kimbladii -Lactobacillus kullabergensis -Lactobacillus melliventris -Lactobacillus sp. -Lactococcus -Lactococcus cremoris -Lactococcus cremoris subsp. cremoris MG1363 -Lactococcus cremoris subsp. cremoris TIFN5 -Lactococcus cremoris subsp. cremoris TIFN6 -Lactococcus cremoris subsp. cremoris TIFN7 -Lactococcus garvieae -Lactococcus garvieae Lg2 -Lactococcus garvieae TB25 -Lactococcus lactis -Lactococcus lactis subsp. lactis -Lactococcus lactis subsp. lactis bv. diacetylactis -Lactococcus lactis subsp. lactis Il1403 -Lactococcus petauri -Lactococcus sp. -Lactuca -Lactuca indica -Lactuca saligna -Lactuca sativa -Lactuca serriola -Lactuca virosa -Ladona fulva -Laelia -Laephotis capensis -Lagenaria -Lagenaria siceraria -Lagenodelphis hosei -Lagenorhynchus acutus -Lagenorhynchus albirostris -Lagenorhynchus obliquidens -Lagerstroemia indica -Lagomorpha -Lagopus lagopus scotica -Lagopus muta -Lagothrix lagotricha -Lagothrix lugens -Lagurus lagurus -Lama glama -Lama guanicoe -Lambdina fiscellaria -Laminaria digitata -Laminaria hyperborea -Lamium album -Lamium amplexicaule -Lamium maculatum -Lamium purpureum -Lampetra fluviatilis -Lamprocapnos spectabilis -Lamprologus kungweensis -Lamprologus lemairii -Lamprologus ocellatus -Lampropeltis californiae -Lampropeltis triangulum hondurensis -Lampsilis cardium -Lampyris noctiluca -Laniidae -Lanius collurio -Lanius cristatus -Lanius ludovicianus -Lanius schach -Lantana camara -Laodelphax striatellus -Laridae -Larimichthys crocea -Larimichthys polyactis -Larinus minutus -Lariophagus distinguendus -Larix griffithii var. speciosa -Larrea tridentata -Larus -Larus argentatus -Larus armenicus -Larus californicus -Larus canus -Larus crassirostris -Larus delawarensis -Larus dominicanus -Larus fuscus -Larus glaucescens -Larus glaucoides -Larus heuglini -Larus hyperboreus -Larus marinus -Larus michahellis -Larus mongolicus -Larus schistisagus -Larus smithsonianus -Larus vegae -Larvivora cyane -Larvivora sibilans -Lasiocampa quercus -Lasiodiplodia sp. YW-2022d -Lasiodiplodia viticola -Lasioglossum -Lasioglossum clypeare -Lasioglossum corvinum -Lasioglossum crassepunctatum -Lasioglossum discum -Lasioglossum glabriusculum -Lasioglossum interruptum -Lasioglossum leucozonium -Lasioglossum malachurum -Lasioglossum marginatum -Lasioglossum pauperatum -Lasioglossum pauxillum -Lasioglossum peregrinum -Lasioglossum politum -Lasioglossum sp. -Lasioglossum villosulum -Lasionycteris noctivagans -Lasiopodomys gregalis -Lasiurus blossevillii -Lasiurus borealis -Lasiurus seminolus -Lasiurus sp. (in: bats) -Lasius neglectus -Lasius niger -Lateolabrax -Lateolabrax japonicus -Lateolabrax maculatus -Lates calcarifer -Lathamus discolor -Lathyrus cicera -Lathyrus ochrus -Lathyrus odoratus -Latilactobacillus curvatus -Latilactobacillus sakei -Latris lineata -Launaea nudicaulis -Lavandula angustifolia -Lavandula stoechas -Lavandula x intermedia -Lavatera -Lebeckia -Leclercia adecarboxylata -Ledebouriella seseloides -Leersia hexandra -Leibnitzia anandria -Leiognathus equula -Leiopotherapon unicolor -Leiothlypis celata -Leiothrix argentauris -Leiothrix lutea -Leishmania aethiopica -Leishmania amazonensis -Leishmania braziliensis -Leishmania braziliensis guyanensis -Leishmania guyanensis -Leishmania infantum -Leishmania lainsoni -Leishmania major -Leishmania martiniquensis -Leishmania naiffi -Leishmania panamensis -Leishmania shawi -Leishmania tropica -Lelliottia -Lelliottia sp. GL2 -Lemmus sibiricus -Lemniscomys rosalia -Lemniscomys striatus -Lemur catta -Lemuridae -Lemyra imparilis -Lemyra phasma -Lens culinaris -Lentibacter -Lentinula edodes -Lentisphaerae bacterium WC36 -Leonotis nepetifolia -Leontocebus nigricollis -Leontopithecus chrysomelas -Leontopithecus rosalia -Leonurus cardiaca -Leonurus japonicus -Leonurus sibiricus -Leopardus geoffroyi -Leopardus guigna -Leopardus guttulus -Leopardus pardalis -Leopardus wiedii -Leopoldamys edwardsi -Leopoldamys neilli -Leopoldamys sabanus -Leopoldia comosa -Lepeophtheirus salmonis -Lepidiolamprologus attenuatus -Lepidium coronopus -Lepidium didymum -Lepidium draba -Lepidium meyenii -Lepidium oleraceum -Lepidium sativum -Lepidochelys kempii -Lepidochelys olivacea -Lepidophthirus macrorihini -Lepidoptera -Lepidoptera sp. -Lepidotrigla alata -Lepidotrigla sp. -Lepilemur mustelinus -Lepomis gibbosus -Lepomis macrochirus -Leporidae -Leptailurus serval -Leptasterias hexactis -Leptobrachium hainanense -Leptocereus quadricostatus -Leptocorisa acuta -Leptolyngbya boryana -Leptolyngbya boryana IU 594 -Leptolyngbya foveolarum -Leptomonas moramango -Leptomonas pyrrhocoris -Leptomonas seymouri -Leptonychotes weddellii -Leptopilina boulardi -Leptoptilos crumeniferus -Leptospira -Leptospira biflexa -Leptospira inadai -Leptotarsus -Leptotila rufaxilla -Leptotrombidium deliense -Leptotrombidium pallidum -Leptuca -Lepus americanus -Lepus californicus -Lepus capensis -Lepus corsicanus -Lepus europaeus -Lepus granatensis -Lepus timidus -Lespedeza procumbens -Lethenteron camtschaticum -Leucaena leucocephala -Leucaena multicapitula -Leucanthemum gaudinii subsp. cantabricum -Leucas martinicensis -Leucas zeylanica -Leucauge argyra -Leuciscus aspius -Leuciscus idus -Leucocoprinus sp. HH-2015c -Leucocoryne -Leucocybe candicans -Leucocytozoon -Leucocytozoon sp. -Leucodon julaceus -Leucoma salicis -Leuconostoc -Leuconostoc falkenbergense -Leuconostoc mesenteroides -Leuconostoc pseudomesenteroides -Leucophaeus atricilla -Leucophaeus modestus -Leucophaeus pipixcan -Leucophaeus scoresbii -Leucopsar rothschildi -Leucosticte brandti -Leucosticte tephrocotis -Leucostoma cinctum -Leuronota fagarae -Leuzea carthamoides -Leveillula taurica -Levilactobacillus brevis -Levilactobacillus brevis ATCC 367 -Liatris -Liatris spicata -Libellula quadrimaculata -Libellula saturata -Liberibacter -Libidibia ferrea -Lichonycteris obscura -Ligia exotica -Ligidium -Ligilactobacillus murinus -Ligularia fischeri -Ligularia stenocephala -Ligusticum chuanxiong -Ligustrum -Ligustrum japonicum -Ligustrum lucidum -Ligustrum obtusifolium -Ligustrum ovalifolium -Ligustrum sinense -Ligustrum vulgare -Lilium -Lilium davidii -Lilium davidii var. unicolor -Lilium distichum -Lilium hybrid cultivar -Lilium hybrid division VII -Lilium lancifolium -Lilium longiflorum -Lilium martagon -Lilium sp. -Limanda limanda -Limatus durhamii -Limatus flavisetosus -Limeum africanum -Limnochromis auritus -Limnodynastes ornatus -Limonium sinuatum -Limosa limosa -Limosilactobacillus fermentum -Limosilactobacillus reuteri -Linaria flavirostris -Lindernia procumbens -Linepithema humile -Linum macraei -Liocarcinus depurator -Liposcelis bostrychophila -Liquorilactobacillus mali -Liriodendron tulipifera -Liriomyza huidobrensis -Liriope muscari -Liriope spicata -Lissonycteris angolensis -Lissonycteris angolensis ruwenzorii -Lissotriton boscai -Lissotriton vulgaris -Listeria -Listeria grayi -Listeria innocua -Listeria ivanovii -Listeria monocytogenes -Listeria monocytogenes ATCC 19115 -Listeria sp. -Listeria weihenstephanensis -Litchi chinensis -Lithobates catesbeianus -Lithobates clamitans -Lithobates grylio -Lithobates palustris -Lithobates pipiens -Lithobates septentrionalis -Lithobates sylvaticus -Lithognathus mormyrus -Lithotoma axillaris -Lithurgus cornutus -Litsea glutinosa -Littorina sp. -Liza parsia -Lobelia -Lobelia cardinalis -Lobelia erinus -Lobelia siphilitica -Locusta migratoria -Loktanella -Lolium -Lolium arundinaceum -Lolium multiflorum -Lolium perenne -Lolium persicum -Lolium rigidum -Lolium sp. -Lomandra longifolia -Lonchitis hirsuta -Lonchorhina aurita -Lonchura -Lonchura atricapilla -Lonchura maja -Lonchura oryzivora -Lonchura punctulata -Lonchura striata -Lonicera caprifolium -Lonicera japonica -Lonomia obliqua -Lontra canadensis -Lontra longicaudis -Lophiomus setigerus -Lophius litulon -Lophocebus albigena -Lophocebus aterrimus -Lophocereus schottii -Lophochroa leadbeateri -Lophodytes cucullatus -Lophophorus impejanus -Lophura erythrophthalma -Lophura leucomelanos -Lophura nycthemera -Lophuromys -Lophuromys aquilus -Lophuromys dudui -Lophuromys laticeps -Lophuromys machangui -Lophuromys nudicaudus -Lophuromys sikapusi -Lophuromys stanleyi -Loramyces juncicola -Loriini -Lorius chlorocercus -Lota lota -Lotidae -Lotus -Lotus corniculatus -Lotus edulis -Lotus halophilus -Loxia curvirostra -Loxioides bailleui -Loxodonta africana -Loxodontomys micropus -Lubomirskia baikalensis -Lucilia sp. (in: flies) -Ludwigia hyssopifolia -Ludwigia linifolia -Ludwigia octovalvis -Ludwigia perennis -Luffa -Luffa acutangula -Luffa aegyptiaca -Luffa hermaphrodita -Luidia maculata -Lunaria annua -Lupinus -Lupinus albus -Lupinus angustifolius -Lupinus cosentinii -Lupinus luteus -Lupinus nootkatensis -Lupinus perennis -Lupinus pilosus -Lupinus polyphyllus -Luscinia -Luteibacter flocculans -Lutjanus campechanus -Lutjanus gibbus -Lutjanus johnii -Lutjanus stellatus -Lutra lutra -Lutraria rhynchaena -Lutrinae -Lutzia halifaxii -Lutzomyia -Lutzomyia evansi -Lutzomyia longipalpis -Lycalopex fulvipes -Lycalopex gymnocercus -Lycalopex vetulus -Lycaon pictus -Lycianthes biflora -Lycianthes rantonnei -Lycium -Lycium barbarum -Lycium chinense -Lycodon rufozonatus -Lycoris aurea -Lycorma delicatula -Lygodium japonicum -Lygus lineolaris -Lygus pratensis -Lymantria dispar -Lymantria dispar asiatica -Lymantria dispar dispar -Lymantria fumida -Lymantria mathura -Lymantria monacha -Lymantria obfuscata -Lymantria xylina -Lymantriinae -Lynx -Lynx canadensis -Lynx canadensis subsolanus -Lynx lynx -Lynx pardinus -Lynx rufus -Lyrurus tetrix -Lysimachia -Lysimachia davurica -Lysimachia foemina -Lysimachia nummularia -Lysinibacillus capsici -Lysinibacillus fusiformis -Lysinibacillus sphaericus C3-41 -Lysiphlebus fabarum -Lytechinus variegatus -Macaca -Macaca arctoides -Macaca assamensis -Macaca balantak -Macaca balantak x tonkeana -Macaca cyclopis -Macaca fascicularis -Macaca fuscata -Macaca fuscata fuscata -Macaca fuscata yakui -Macaca leonina -Macaca maura -Macaca mulatta -Macaca nemestrina -Macaca radiata -Macaca silenus -Macaca sp. -Macaca sylvanus -Macaca thibetana -Macaca tonkeana -Maccullochella peelii -Maclura tricuspidata -Macomangulus tenuis -Macrobrachium nipponense -Macrobrachium rosenbergii -Macrobrachium sp. -Macrocentrus marginator -Macrocystis pyrifera -Macroglossus -Macroglossus minimus -Macroglossus sobrinus -Macrognathus aculeatus -Macronectes -Macronectes giganteus -Macronycteris commersoni -Macronycteris gigas -Macronycteris vittatus -Macrophomina phaseolina -Macropiper -Macropodidae -Macropodus opercularis -Macropsylla hercules -Macroptilium -Macroptilium atropurpureum -Macroptilium bracteatum -Macroptilium erythroloma -Macroptilium gracile var. longepedunculatum -Macroptilium lathyroides -Macropus fuliginosus -Macropus giganteus -Macropus sp. -Macropygia phasianella -Macroramphosus scolopax -Macrosiphum euphorbiae -Macrostomum lignano -Macrotermes carbonarius -Macrotus californicus -Macrotus waterhousii -Macrotyloma uniflorum -Macrourus berglax -Mactra chinensis -Mactra quadrangularis -Magnolia tripetala -Mahasena corbetti -Malachra -Malachra alceifolia -Malachra capitata -Malachra fasciata -Malacocephalus occidentalis -Malacochersus tornieri -Malacomys -Malacomys longipes -Malacorhynchus membranaceus -Malacosoma -Malacosoma americanum -Malacosoma californicum -Malacosoma neustria -Malacostraca -Malakichthys elegans -Malassezia restricta -Malassezia sympodialis -Malayopython reticulatus -Malayopython timoriensis -Mallotus japonicus -Malurus cyaneus -Malus -Malus asiatica -Malus domestica -Malus micromalus -Malus prunifolia -Malus pumila -Malus sieversii -Malus sp. -Malus spectabilis -Malus sylvestris -Malus x platycarpa -Malva -Malva cretica -Malva crispa -Malva linnaei -Malva neglecta -Malva nicaeensis -Malva parviflora -Malva sylvestris -Malva verticillata -Malvaceae -Malvastrum -Malvastrum americanum -Malvastrum coromandelianum -Malvaviscus arboreus -Malvaviscus penduliflorus -Malvoideae -Mamestra brassicae -Mamestra configurata -Mammalia -Mammaliicoccus lentus -Mammaliicoccus sciuri -Mammaliicoccus vitulinus -Mammuthus -Mandevilla -Mandevilla sanderi -Mandragora autumnalis -Mandrillus leucophaeus -Mandrillus sphinx -Manduca sexta -Mangifera indica -Manihot -Manihot esculenta -Manihot glaziovii -Manis javanica -Manis pentadactyla -Manis pentadactyla pentadactyla -Mannheimia haemolytica -Manorina melanocephala -Mansonia -Mansonia africana -Mansonia humeralis -Mansonia pseudotitillans -Mansonia septempunctata -Mansonia titillans -Mansonia uniformis -Mansonia wilsoni -Mantis religiosa -Mantispinae sp. -Manulea altissima -Maoriblatta novaeseelandiae -Maranta arundinacea -Maranta leuconeura -Marchantiophyta -Mareca -Mareca americana -Mareca falcata -Mareca penelope -Mareca sibilatrix -Mareca strepera -Margaritifera falcata -Maribacter forsetii -marine bacterium HIMB624 -Marinitoga camini -Marinobacter -Marinomonas -Marinomonas mediterranea -Marinomonas sp. -Markhamia zanzibarica -Marmosa demerarae -Marmosa murina -Marmosa paraguayana -marmosets -Marmota caudata -Marmota flaviventris -Marmota himalayana -Marmota marmota -Marmota monax -Marmotini -Marsdenia floribunda -Martes -Martes americana -Martes foina -Martes martes -Martes zibellina -Masdevallia -Masdevallia schroederiana -Mastigocladus sp. -Mastomys -Mastomys awashensis -Mastomys coucha -Mastomys erythroleucus -Mastomys natalensis -Mastomys sp. -Mastotermes darwiniensis -Matricaria chamomilla var. recutita -Matricaria discoidea -Matsumuraeses phaseoli -Matthiola -Matthiola incana -Mauremys megalocephala -Mauremys sinensis -Maxillaria luteograndiflora -Maxomys surifer -Maxomys whiteheadi -Mayetiola destructor -Mazama nana -Mazus reptans -Meccus longipennis -Medauroidea extradentata -Mediaster aequalis -Medicago arborea -Medicago littoralis x Medicago truncatula -Medicago lupulina -Medicago polymorpha -Medicago sativa -Megachile albisecta -Megachile centuncularis -Megachile circumcincta -Megachile ericetorum -Megachile leachella -Megachile melanopyga -Megachile pilidens -Megachile rotundata -Megachile sculpturalis -Megachile willughbiella -Megacollybia platyphylla -Megacrania phelaus -Megaderma -Megaderma lyra -Megadyptes antipodes -Megaerops ecaudatus -Megaerops kusnotoi -Megaerops niphanae -Megaloglossus woermanni -Megalographa biloba -Megaptera novaeangliae -Megascolecidae -Megascolia maculata flavifrons -Megascops choliba -Megastigmus spermotrophus -Megathyrsus infestus -Megathyrsus maximus -Megathyrsus trichocladum -Meiothermus sp. -Melampyrum roseum -Melanchra persicariae -Melanconiella sp. -Melanerpes carolinus -Melanitta -Melanitta americana -Melanitta fusca -Melanitta nigra -Melanitta perspicillata -Melanochromis auratus -Melanoconion -Melanogrammus aeglefinus -Melanospiza bicolor -Melanostoma -Melanostoma mellinum -Melanotaenia fluviatilis -Melastoma malabathricum -Meleagris -Meleagris gallopavo -Meleagris gallopavo intermedia -Meleagris gallopavo merriami -Meleagris gallopavo silvestris -Meles anakuma -Meles leucurus -Meles meles -Melia azedarach -Melilotus -Melilotus dentatus -Melilotus indicus -Melilotus officinalis -Melilotus officinalis subsp. suaveolens -Melinis repens -Melipona quadrifasciata anthidioides -Melipona quadrifasciata quadrifasciata -Melipona scutellaris -Melissa officinalis -Melitta haemorrhoidalis -Melittomma -Melitturga clavicornis -Mellivora capensis -Melochia -Melogale -Melogale moschata -Melolontha melolontha -Melomys -Melomys burtoni -Melophagus ovinus -Melopsittacus undulatus -Melospiza melodia -Melothria pendula -Melozone crissalis -Melursus ursinus -Menetes -Menetes berdmorei -Menevia lucara -Mentha -Mentha arvensis -Mentha canadensis -Mentha requienii -Mentha spicata -Mentha x gracilis -Mentha x piperita -Mephitidae -Mephitis -Mephitis macroura -Mephitis mephitis -Mercurialis annua -Meretrix meretrix -Mergellus albellus -Mergus -Mergus merganser -Mergus squamatus -Meriones libycus -Meriones libycus erythrourus -Meriones meridianus -Meriones shawi -Meriones tamariscinus -Meriones unguiculatus -Merlangius merlangus -Merluccius productus -Merodon -Merodon fulcratus -Meroplius fasciculatus -Merops apiaster -Merops ornatus -Merostomata -Mertensia paniculata -Mertensia virginica -Mesocricetus -Mesocricetus auratus -Mesophylla macconnelli -Mesoplodon bidens -Mesoplodon densirostris -Mesoplodon europaeus -Mesoplodon stejnegeri -Mesorhizobium loti -Mesosphaerum pectinatum -Mespilus germanica -Messor concolor -Metallosphaera prunae -Metallosphaera sedula -Metallosphaera sp. -Metamycoplasma arthritidis -Metapenaeopsis dalei -Metapenaeopsis lamellata -Metapenaeus affinis -Metapenaeus ensis -Metapenaeus joyneri -Metaphire sieboldi -Metarhizium anisopliae -Metarhizium brunneum -Metarhizium flavoviride -Metatheria -Metazoa -Metellina curtisi -Methanobacterium formicicum -Methanocaldococcus fervens -Methanoculleus bourgensis -Methanophagales -Methanosarcina sp. -Methanothermobacter -Methanothermobacter thermautotrophicus -Methylophilaceae bacterium IMCC19250 -Methylophilales bacterium -Methylophilales bacterium H5P1 -Metorchis orientalis -Meuschenia flavolineata -Miathyria marcella -Micaelamys namaquensis -Mico melanurus -Micractinium conductrix -Micrarchus hystriculeus -Micrarchus sp. n. 2 LD-2013 -Microbacterium -Microbacterium foliorum -Microbacterium liquefaciens -Microbacterium natoriense -Microbacterium nematophilum -Microbacterium oxydans -Microbacterium paraoxydans -Microbacterium radiodurans -Microbacterium sp. -Microbacterium sp. R1 -Microbacterium terrae -Microbacterium testaceum -Microcanthus strigatus -Microcarbo coronatus -Microcarbo niger -Microcebus griseorufus -Microcebus murinus -Microcebus sp. hybrid TV-2023 -Microcerotermes -Microchiroptera -Microctonus hyperodae -Microcystis -Microcystis aeruginosa -Microcystis aeruginosa FACHB-469 -Microcystis aeruginosa FACHB-942 -Microcystis elabens -Microcystis sp. -Microdochium albescens -Microeca fascinans -Microgale cowani -Microgale gymnorhyncha -Microgale jobihely -Microgale longicaudata -Microgale majori -Microgale principula -Microgale taiva -Microhyla fissipes -Microhyla pulchra -Microlaena stipoides -Microlicia parviflora -Micromesistius poutassou -Micromonas -Micromonas commoda -Micromonas polaris -Micromonas pusilla -Micromonas sp. -Micromonas sp. SAG8 -Micromonospora carbonacea -Micromonospora sp. ATCC 39149 -Micromys minutus -Microphallus -Microplitis demolitor -Microplitis mediator -Microplitis pennatulae -Microplitis similis -Micropogonias furnieri -Micropterus dolomieu -Micropterus salmoides -Microstomus kitt -Microstomus pacificus -Microtus agrestis -Microtus arvalis -Microtus californicus -Microtus dogramacii -Microtus duodecimcostatus -Microtus fortis -Microtus guentheri -Microtus majori -Microtus maximowiczii -Microtus maximowiczii ungurensis -Microtus montanus -Microtus obscurus -Microtus ochrogaster -Microtus pennsylvanicus -Microtus rossiaemeridionalis -Microtus socialis -Microtus subterraneus -Microvirgula aerodenitrificans -Mideopsis sp. -Mikania micrantha -Mikrogeophagus ramirezi -Millingtonia hortensis -Miltonia -Milvus migrans -Milvus milvus -Mimidae -Mimomyia splendens -Mimosa -Mimosa pudica -Mimosa sensitiva -Mimus -Mimus parvulus -Mimus polyglottos -Miniopterus -Miniopterus africanus -Miniopterus australis -Miniopterus fuliginosus -Miniopterus fuscus -Miniopterus gleni -Miniopterus griveaudi -Miniopterus inflatus -Miniopterus magnater -Miniopterus mahafaliensis -Miniopterus manavi -Miniopterus minor -Miniopterus mossambicus -Miniopterus natalensis -Miniopterus orianae oceanensis -Miniopterus pusillus -Miniopterus schreibersii -Miniopterus sororculus -Minous monodactylus -Miopithecus ogouensis -Miopithecus talapoin -Mirabilis -Mirabilis jalapa -Mirounga angustirostris -Miscanthus -Miscanthus sinensis -Miscanthus x giganteus -Misgurnus anguillicaudatus -Mitu mitu -Mizuhopecten yessoensis -Mnemiopsis leidyi -Mniotilta varia -Mocis -Mollugo verticillata -Molossidae -Molossops neglectus -Molossops temminckii -Molossus -Molossus coibensis -Molossus currentium -Molossus molossus -Molossus pretiosus -Molossus rufus -Molossus sinaloae -Molossus sp. -Molothrus -Molothrus ater -Momordica balsamina -Momordica charantia -Momordica dioica -Momordica subangulata subsp. renigera -Monachus monachus -Monarda didyma -Moniezia expansa -Monilinia fructicola -Monilinia fructigena -Moniliophthora roreri -Monoclea gottschei -Monodelphis iheringi -Monodon monoceros -Monolepta lauta -Monopterus albus -Monoraphidium neglectum -Monosapyga clavicornis -Monosiga brevicollis ATCC 50154 -Monotropa uniflora -Monstera adansonii -Montifringilla henrici -Montipora hispida -Mops -Mops condylurus -Mops demonstrator -Mops leucostigma -Mops midas -Mops pumilus -Moraxella catarrhalis -Morchella esculenta -Morchella importuna -Morelia bredli -Morelia carinata -Morelia spilota -Morelia spilota mcdowelli -Morelia spilota metcalfei -Morelia spilota spilota -Morelia viridis -Morella rubra -Morganella -Morganella morganii -Morganella sp. (in: enterobacteria) -Morinda citrifolia -Moringa oleifera -Mormopterus acetabulosus -Mormopterus jugularis -Mormopterus sp. BBvV-2008 -Morone americana -Morone chrysops -Morone saxatilis -Morone saxatilis x Morone chrysops -Morus -Morus alba -Morus bassanus -Morus nigra -Morus rubra -Moschus berezovskii -Moschus chrysogaster -Motacilla -Motacilla alba -Motacilla cinerea -Mucor hiemalis -Mucor irregularis -Mucorales -Mucuna -Mucuna pruriens -Mucuna pruriens var. utilis -Mugil cephalus -Mugilogobius abei -Mullus barbatus -Mullus barbatus barbatus -Mullus sp. -Mullus surmuletus -Muntiacus reevesi -Muntingia calabura -Murex trapa -Murina aenea -Murina aurata -Murina cyclotis -Murina hilgendorfi -Murina leucogaster -Murina ussuriensis -Murinae gen. sp. TG-2020 -Murraya koenigii -Mus -Mus baoulei -Mus booduga -Mus bufo -Mus caroli -Mus cervicolor -Mus cookii -Mus mattheyi -Mus minutoides -Mus musculoides -Mus musculus -Mus musculus castaneus -Mus musculus domesticus -Mus musculus molossinus -Mus musculus musculus -Mus pahari -Mus setulosus -Mus sp. -Mus sp. CL-2019 -Mus sp. TG-2020 -Mus spicilegus -Mus spretus -Mus terricolor -Mus triton -Musa -Musa AAAB Group -Musa AAB Group -Musa AB Group -Musa ABB Group -Musa acuminata -Musa acuminata AAA Group -Musa balbisiana -Musa basjoo -Musa hybrid cultivar -Musa itinerans -Musa laterita -Musa paracoccinea -Musa sp. -Musa textilis -Musa x paradisiaca -Musca domestica -Musca vetustissima -Muscardinus avellanarius -Muscari -Muscari neglectum -Muscari sp. -Muscicapa -Muscicapa latirostris -Muscicapa striata -Muscicapidae -Muscidae -Muscina stabulans -Mustela erminea -Mustela eversmannii -Mustela kathiah -Mustela lutreola -Mustela nivalis -Mustela putorius -Mustela putorius furo -Mustela sibirica -Mustela sp. -Mustelidae -Mustelus manazo -Mycetophilidae -Mycetophylax faunulus -Mycobacterium -Mycobacterium avium -Mycobacterium sp. -Mycobacterium tuberculosis -Mycobacteroides abscessus -Mycobacteroides abscessus subsp. bolletii F1725 -Mycobacteroides chelonae -Mycolicibacterium aichiense -Mycolicibacterium phlei -Mycolicibacterium smegmatis -Mycolicibacterium smegmatis MC2 155 -Mycoplasma -Mycoplasma anserisalpingitidis -Mycoplasma sp. -Mycoplasmopsis anatis -Mycoplasmopsis pulmonis -Mycosphaerellaceae sp. -Mycteroperca -Myiarchus tyrannulus -Myiobius barbatus -Myiopsitta monachus -Myliobatis tobijei -Myocastor coypus -Myodes -Myodes glareolus -Myodes regulus -Myodes rufocanus -Myodes rufocanus bedfordiae -Myodes rutilus -Myonycteris -Myonycteris torquata -Myophonus insularis -Myosorex geata -Myosorex zinki -Myosotis -Myosoton aquaticum -Myospalax psilurus -Myotis -Myotis adversus -Myotis albescens -Myotis alcathoe -Myotis altarium -Myotis aurascens -Myotis austroriparius -Myotis bechsteinii -Myotis blythii -Myotis bombinus -Myotis brandtii -Myotis californicus -Myotis capaccinii -Myotis cf. californicus/ciliolabrum BL-2021 -Myotis chiloensis -Myotis chinensis -Myotis ciliolabrum -Myotis crypticus -Myotis dasycneme -Myotis daubentonii -Myotis davidii -Myotis emarginatus -Myotis escalerai -Myotis evotis -Myotis fimbriatus -Myotis flavus -Myotis frater -Myotis goudoti -Myotis horsfieldii -Myotis ikonnikovi -Myotis keaysi -Myotis keenii -Myotis laniger -Myotis leibii -Myotis levis -Myotis longipes -Myotis lucifugus -Myotis macrodactylus -Myotis macropus -Myotis muricola -Myotis myotis -Myotis myotis/blythii -Myotis mystacinus -Myotis nattereri -Myotis nigricans -Myotis oxygnathus -Myotis oxyotus -Myotis pequinius -Myotis petax -Myotis punicus -Myotis ricketti -Myotis riparius -Myotis septentrionalis -Myotis siligorensis -Myotis sp. -Myotis thysanodes -Myotis velifer -Myotis volans -Myotis welwitschii -Myotis yumanensis -Myotomys unisulcatus -Myoxocephalus octodecemspinosus -Myriapoda -Myriodontium keratinophilum -Myrmecophaga tridactyla -Myrmeleon formicarius -Myrmica rubra -Myrmica scabrinodis -Myrmicocrypta -Myrmoderus ferrugineus -Myrmotherula longipennis -Myrrophis chinensis -Mystacina tuberculata -Mystus gulio -Mythimna -Mythimna separata -Mythimna sequax -Mythimna unipuncta -Mytilus coruscus -Mytilus edulis -Mytilus galloprovincialis -Mytilus sp. -Myuchelys georgesi -Myuchelys latisternum -Myxococcus -Myxococcus xanthus -Myzus persicae -Myzus persicae nicotianae -Nadzikambia mlanjensis -Naemorhedus goral -Nageia nagi -Naja atra -Naja siamensis -Nandina domestica -Nandinia binotata -Nannochloropsis oceanica -Nannochloropsis oculata -Nannospalax galili -Nanohaloarchaea archaeon AB578-D14 -Nanonycteris veldkampii -Nanorana parkeri -Naranga aenescens -Narcissus -Narcissus cyclamineus -Narcissus jonquilla -Narcissus papyraceus -Narcissus pseudonarcissus -Narcissus tazetta -Narcissus tazetta subsp. chinensis -Nasalis larvatus -Nasonia giraulti -Nasonia vitripennis -Nasturtium officinale -Nasua -Nasua narica -Nasua nasua -Natalus lanatus -Natrialba -Natrialba magadii -Natrialba magadii ATCC 43099 -Natrinema sp. J7-1 -Natrinema thermotolerans -Natrinema versiforme -Natrix maura -Natrix natrix -Neacomys musseri -Neacomys spinosus -Nebalia bipes -Neckera douglasii -Necromys benefactus -Necromys lasiurus -Necromys obscurus -Necrosyrtes monachus -Nectomys squamipes -Negaprion brevirostris -Neisseria meningitidis -Nelumbo nucifera -Nematalosa erebi -Nematanthus nervosus -Nematoda -Nemesia -Nemesia fruticans -Nemipterus randalli -Nemipterus virgatus -Nemophora degeerella -Neoaliturus haematoceps -Neoaliturus tenellus -Neochen jubata -Neochmia temporalis -Neoconocephalus -Neodiprion abietis -Neodiprion lecontei -Neodiprion sertifer -Neodon clarkei -Neodon fuscus -Neodon leucurus -Neofelis nebulosa -Neofusicoccum luteum -Neofusicoccum parvum -Neogale vison -Neognathae -Neogobius melanostomus -Neohelice granulata -Neohydatothrips variabilis -Neolamarckia cadamba -Neolamprologus -Neolamprologus brevis -Neolamprologus buescheri -Neolamprologus caudopunctatus -Neolamprologus fasciatus -Neolamprologus furcifer -Neolamprologus multifasciatus -Neolamprologus niger -Neolamprologus savoryi -Neolamprologus tetracanthus -Neolamprologus toae -Neolamprologus walteri -Neomarica northiana -Neomonachus schauinslandi -Neomys anomalus -Neomys fodiens -Neomysis awatschensis -Neophasia -Neophema chrysogaster -Neophema pulchella -Neophema splendida -Neophocaena asiaeorientalis asiaeorientalis -Neopomacentrus bankieri -Neoporphyra dentata -Neoporphyra haitanensis -Neopsephotus bourkii -Neopyropia tenera -Neopyropia yezoensis -Neoromicia -Neoromicia brunneus -Neoromicia helios -Neoromicia somalicus -Neoromicia tenuipinnis -Neoscirrhia matteucciicola -Neoscona nautica -Neosmilaster georgianus -Neotoma -Neotoma albigula -Neotoma cinerea -Neotoma lepida -Neotoma leucodon -Neotoma macrotis -Neotoma mexicana -Neotoma micropus -Nepenthes alata -Nepenthes mirabilis -Nepeta cataria -Nephelomys albigularis -Nephelomys devius -Nephotettix cincticeps -Nepytia phantasmaria -Nereididae -Nerine -Nerine bowdenii -Nerium oleander -Nerodia floridana -Nerodia taxispilota -Nesidiocoris tenuis -Nesogale dobsoni -Nestor notabilis -Netta peposaca -Netta rufina -Neurachne minor -Neurergus crocatus -Neurospora crassa -Neurospora discreta -Neurospora intermedia -Neurotrichus gibbsii -Neustanthus phaseoloides -Nezara viridula -Nicandra physalodes -Nicotiana -Nicotiana alata -Nicotiana benthamiana -Nicotiana cavicola -Nicotiana clevelandii -Nicotiana glauca -Nicotiana glutinosa -Nicotiana mutabilis -Nicotiana occidentalis -Nicotiana occidentalis subsp. hesperis -Nicotiana rustica -Nicotiana sp. -Nicotiana sylvestris -Nicotiana tabacum -Nicotiana velutina -Nicotiana x edwardsonii -Nigrospora chinensis -Nigrospora oryzae -Nigrospora sphaerica -Nilaparvata lugens -Ninox boobook -Ninox novaeseelandiae -Ninox strenua -Nippancistroger testaceus -Nipponanthemum nipponicum -Nipponia nippon -Nisaetus nipalensis -Nitratiruptor sp. SB155-2 -Nitratiruptor sp. YY08-10 -Nitratiruptor sp. YY08-13 -Nitratiruptor sp. YY08-14 -Nitratiruptor sp. YY08-26 -Nitrincola -Nitrosomonadales -Nitrosopumilus sp. -Nitrososphaera viennensis EN76 -Nitrososphaeria -Nitzschia reversa -Niumbaha superba -Niviventer confucianus -Niviventer coninga -Niviventer cremoriventer -Niviventer eha -Niviventer excelsior -Niviventer fulvescens -Niviventer huang -Niviventer niviventer -Niviventer sp. -Nocardia -Nocardia asteroides -Nocardia brasiliensis -Nocardia carnea -Nocardia seriolae -Nocardia transvalensis -Nodularia -Nodularia douglasiae -Nodularia spumigena -Nodularia spumigena kac68 -Nomada distinguenda -Nomada lathburiana -Nomascus gabriellae -Nomascus leucogenys -Nonlabens -Nopalea cochenillifera -Northiella haematogaster -Nostoc -Nostoc sp. -Nostoc sp. PCC 7120 = FACHB-418 -Notamacropus agilis -Notamacropus rufogriseus -Notemigonus crysoleucas -Noterus clavicornis -Notophthalmus viridescens -Notropis atherinoides -Novacetimonas maltaceti -Novosphingobium -Nucella lapillus -Numenius -Numenius arquata -Numenius phaeopus -Numida -Numida meleagris -Numididae -Numididae sp. -Nyctalus lasiopterus -Nyctalus leisleri -Nyctalus noctula -Nyctalus plancyi -Nyctalus velutinus -Nyctereutes -Nyctereutes procyonoides -Nycteribia kolenatii -Nycteribia schmidlii -Nycteribiidae -Nycteridae -Nycteris -Nycteris grandis -Nycteris hispida -Nycteris macrotis -Nycteris thebaica -Nycteris tragata -Nycticebus coucang -Nycticeinops schlieffeni -Nycticeius humeralis -Nycticorax -Nycticorax nycticorax -Nyctimene cephalotes -Nyctinomops -Nyctinomops femorosaccus -Nyctinomops laticaudatus -Nyctinomops macrotis -Nyctophilus geoffroyi -Nyctophilus gouldi -Nylanderia fulva -Nymphaea alba -Nymphalis c-album -Nymphalis io -Nymphalis urticae -Nymphicus hollandicus -Nymphoides peltata -Nyssomyia flaviscutellata -Nyssomyia trapidoi -Nyssomyia umbratilis -Nyssomyia ylephiletor -Occasitermes -Oceanodroma homochroa -Oceanospirillum -Oceanospirillum sanctuarii -Ochlerotatus -Ochlerotatus abserratus -Ochlerotatus aculeatus -Ochlerotatus aff. punctor/punctodes -Ochlerotatus albifasciatus -Ochlerotatus albineus -Ochlerotatus angustivittatus -Ochlerotatus atlanticus -Ochlerotatus bancroftianus -Ochlerotatus berlandi -Ochlerotatus caballus -Ochlerotatus campestris -Ochlerotatus camptorhynchus -Ochlerotatus canadensis -Ochlerotatus cantans -Ochlerotatus cantator -Ochlerotatus caspius -Ochlerotatus cataphylla -Ochlerotatus cf. punctor/punctodes -Ochlerotatus clelandi -Ochlerotatus communis -Ochlerotatus cyprius -Ochlerotatus detritus -Ochlerotatus diantaeus -Ochlerotatus dorsalis -Ochlerotatus eidsvoldensis -Ochlerotatus excrucians -Ochlerotatus flavescens -Ochlerotatus fulvus -Ochlerotatus harrisoni -Ochlerotatus hesperonotius -Ochlerotatus hexodontus -Ochlerotatus infirmatus -Ochlerotatus intrudens -Ochlerotatus macintoshi -Ochlerotatus multiplex -Ochlerotatus nigripes -Ochlerotatus normanensis -Ochlerotatus procax -Ochlerotatus pseudonormanensis -Ochlerotatus pullatus -Ochlerotatus punctor -Ochlerotatus sagax -Ochlerotatus scapularis -Ochlerotatus serratus -Ochlerotatus sierrensis -Ochlerotatus sollicitans -Ochlerotatus sp. -Ochlerotatus spencerii -Ochlerotatus squamiger -Ochlerotatus sticticus -Ochlerotatus subdiversus -Ochlerotatus taeniorhynchus -Ochlerotatus terrens -Ochlerotatus theobaldi -Ochlerotatus triseriatus -Ochlerotatus trivittatus -Ochlerotatus vigilax -Ochlerotatus vittiger -Ochotona alpina -Ochotona cansus -Ochotona curzoniae -Ochotona sp. -Ochotona thibetana -Ochotonidae -Ochrobactrum -Ochrobactrum sp. POC9 -Ochthera mantis -Ocimum -Ocimum basilicum -Ocimum campechianum -Ocimum gratissimum -Ocimum kilimandscharicum -Ocimum tenuiflorum -Octadecabacter -Octolasmis neptuni -Octopus -Ocyphaps lophotes -Ocypode cordimanus -Odobenus rosmarus -Odobenus rosmarus divergens -Odobenus rosmarus rosmarus -Odocoileus hemionus -Odocoileus hemionus columbianus -Odocoileus hemionus sitkensis -Odocoileus virginianus -Odonata -Odontotermes -Odontotermes wallonensis -Odontothrips loti -Odorrana tormota -Odynerus -Oeciacus vicarius -Oecomys auyantepui -Oecomys bicolor -Oecomys rutilus -Oehlia diaphana -Oena capensis -Oenanthe isabellina -Oenanthe javanica -Oenococcus -Oenococcus oeni -Oenomys hypoxanthus -Oenothera laciniata -Oidiodendron maius -Okamejei acutispina -Okanagana villosa -Okapia johnstoni -Olea -Olea europaea -Olene mendosa -Oligodon formosanus -Oligoryzomys chacoensis -Oligoryzomys costaricensis -Oligoryzomys flavescens -Oligoryzomys fornesi -Oligoryzomys fulvescens -Oligoryzomys longicaudatus -Oligoryzomys mattogrossae -Oligoryzomys microtis -Oligoryzomys nigripes -Oligoryzomys sp. -Oligoryzomys sp. RT-2012 -Oligoryzomys utiaritensis -Oligoryzomys vegetus -Olleya sp. HaHaR_3_96 -Omphalodes -Oncidium -Oncidium hybrid cultivar -Oncidium maculatum -Oncopera intricoides -Oncorhynchus clarkii -Oncorhynchus clarkii virginalis -Oncorhynchus gilae -Oncorhynchus gilae apache -Oncorhynchus gorbuscha -Oncorhynchus keta -Oncorhynchus kisutch -Oncorhynchus masou -Oncorhynchus masou ishikawae -Oncorhynchus masou masou -Oncorhynchus mykiss -Oncorhynchus mykiss aguabonita -Oncorhynchus mykiss gairdneri -Oncorhynchus nerka -Oncorhynchus nerka adonis -Oncorhynchus tshawytscha -Ondatra zibethicus -Oniscidea -Onopordum -Onopordum cyprium -Onthophagus similis -Onychomys torridus -Onychoprion fuscatus -Onychostruthus taczanowskii -Oophaga pumilio -Operophtera bruceata -Operophtera brumata -Opheodrys aestivus -Opheodrys vernalis -Ophiocordyceps sinensis -Ophiostoma bicolor -Ophiostoma himal-ulmi -Ophiostoma minus -Ophiostoma novo-ulmi -Ophiusa disjungens -Ophrys fusca subsp. iricolor -Ophthalmotilapia ventralis -Opisthorchis felineus -Oplegnathus fasciatus -Oplegnathus punctatus -Oplismenus burmannii -Opsiphanes invirae -Opuntia -Opuntia albicarpa (nom. inval.) -Opuntia arenaria -Opuntia atrispina -Opuntia auberi -Opuntia aureispina -Opuntia basilaris -Opuntia boldinghii -Opuntia brasiliensis -Opuntia bravoana -Opuntia caracassana -Opuntia carstenii -Opuntia cespitosa -Opuntia chaffeyi -Opuntia discolor -Opuntia echios var. echios -Opuntia engelmannii -Opuntia engelmannii var. aciculata -Opuntia engelmannii var. lindheimeri -Opuntia engelmannii var. linguiformis -Opuntia ficus-indica -Opuntia guatemalensis -Opuntia hondurensis -Opuntia inaperta -Opuntia karwinskiana -Opuntia mackensenii -Opuntia martiniana -Opuntia microdasys -Opuntia parviclada -Opuntia phaeacantha -Opuntia puberula -Opuntia robusta -Opuntia rufida -Opuntia santa-rita -Opuntia stenopetala -Opuntia streptacantha -Opuntia tapona -Opuntia tuna -Opuntia x andersonii -Opuntia x rooneyi -Orchesella cincta -Orchidaceae -Orchis hatagirea -Orchis militaris -Orchis simia -Orcinus orca -Oreamnos americanus -Oreina cacaliae -Oreochromis -Oreochromis aureus x Oreochromis niloticus -Oreochromis mossambicus -Oreochromis niloticus -Oreochromis niloticus x Oreochromis aureus -Oreochromis sp. YC-2004 -Oreolalax rhodostigmatus -Orgyia antiqua -Orgyia pseudotsugata -Orgyia vetusta -Orientallactaga sibirica -Oriolus chinensis -Oriolus flavocinctus -Oriolus oriolus -Orisarma dehaani -Orisarma intermedium -Orithyia sinica -Orius niger -Orius sauteri -Ornithodoros -Ornithodoros alactagalis -Ornithodoros asperus -Ornithodoros compactus -Ornithodoros coriaceus -Ornithodoros erraticus -Ornithodoros moubata -Ornithodoros phacochoerus -Ornithodoros porcinus -Ornithodoros porcinus porcinus -Ornithodoros savignyi -Ornithodoros tartakovskyi -Ornithodoros waterbergensis -Ornithogalum -Ornithogalum cuspidatum -Ornithogalum thyrsoides -Ornithonyssus bursa -Orobanche cernua var. cumana -Oropsylla silantiewi -Ortalis vetula -Orthetrum albistylum -Orthetrum chrysostigma -Orthetrum sabina -Orthetrum testaceum -Orthomeria sp. -Orthoptera -Orthosiphon aristatus -Ortmanniana ligamentina -Ortmanniana pectorosa -Orussus unicolor -Orychophragmus violaceus -Oryctes rhinoceros -Oryctolagus cuniculus -Oryctolagus cuniculus algirus -Oryctolagus cuniculus cuniculus -Oryx -Oryx dammah -Oryx gazella -Oryx leucoryx -Oryza -Oryza longistaminata -Oryza rufipogon -Oryza sativa -Oryza sativa Japonica Group -Oryza sp. -Oryzoborus crassirostris -Oryzomys -Oryzomys couesi -Oryzomys palustris -Oryzomys sp. -Osedax japonicus -Osmerus mordax -Osmia aurulenta -Osmia bicornis -Osmia brevicornis -Osmia caerulescens -Osmia cornuta -Osmia rufohirta -Osmia taurus -Osphronemus goramy -Osteospermum -Osteospermum fruticosum -Ostichthys japonicus -Ostracion cubicus -Ostreidae -Ostreobium -Ostreococcus -Ostreococcus mediterraneus -Ostreococcus sp. -Ostreococcus sp. 'lucimarinus' -Ostreococcus sp. RCC344 -Ostreococcus sp. RCC356 -Ostreococcus sp. SAG12 -Ostreococcus tauri -Ostrinia furnacalis -Otaria byronia -Otariidae -Otis tarda -Otobius megnini -Otocolobus manul -Otocyon megalotis -Otolemur crassicaudatus -Otomops harrisoni -Otomops madagascariensis -Otomops martiensseni -Otomys tropicalis -Otostigmus scaber -Otus -Otus scops -Ovibos moschatus -Ovis -Ovis ammon -Ovis aries -Ovis aries musimon -Ovis canadensis -Ovis dalli -Ovis dalli stonei -Ovis orientalis -Oxalis -Oxalis corniculata -Oxalis corymbosa -Oxalis debilis -Oxalis drummondii -Oxalis latifolia -Oxalis triangularis -Oxalis tuberosa -Oxera neriifolia -Oxya chinensis -Oxya yezoensis -Oxybasis rubra -Oxybelus bipunctatus -Oxyeleotris lineolata -Oxyeleotris marmorata -Oxymycterus -Oxymycterus judex -Oxymycterus nasutus -Oxymycterus rufus -Oxypetalum -Oxyplax ochracea -Oxyura australis -Oxyura jamaicensis -Ozimops sp. DP-2019 -Pachycereus -Pachycladon fastigiatum -Pachycrepoideus vindemmiae -Pachydiplax longipennis -Pachyrhizus -Pachyrhizus erosus -Pachysandra -Pachytrina philargyria -Pachytriton brevipes -Pacifastacus leniusculus -Paederia scandens -Paederus fuscipes -Paenibacillus -Paenibacillus dendritiformis -Paenibacillus glucanolyticus -Paenibacillus larvae -Paenibacillus polymyxa -Paeniglutamicibacter sulfureus -Paeonia -Paeonia lactiflora -Paeonia officinalis -Paeonia suffruticosa -Pagellus -Pagellus acarne -Pagellus erythrinus -Pagrus auratus -Pagrus auriga -Pagrus major -Pagrus pagrus -Paguma larvata -Paguroidea -Palaemon -Palaemon gravieri -Palaemon kadiakensis -Palaemon mundusnovus -Palaemon orientis -Pallavicinia lyellii -Palpita vitrealis -Pampus argenteus -Pampus punctatissimus -Pan paniscus -Pan troglodytes -Pan troglodytes ellioti -Pan troglodytes schweinfurthii -Pan troglodytes troglodytes -Pan troglodytes verus -Panax ginseng -Panax notoginseng -Pandanus -Pandanus amaryllifolius -Pandemis limitata -Pandion haliaetus -Pangasianodon hypophthalmus -Panicum coloratum -Panicum dichotomiflorum -Panicum ecklonii -Panicum miliaceum -Panicum sp. -Panicum sumatrense -Panicum virgatum -Panolis flammea -Panonychus citri -Pantala flavescens -Pantala hymenaea -Panthera leo -Panthera leo leo -Panthera leo persica -Panthera onca -Panthera pardus -Panthera pardus fusca -Panthera pardus orientalis -Panthera tigris -Panthera tigris altaica -Panthera tigris amoyensis -Panthera tigris jacksoni -Panthera tigris tigris -Panthera uncia -Pantherina griselda -Pantherophis guttatus -Pantherophis obsoletus -Pantholops hodgsonii -Pantodon buchholzi -Pantoea -Pantoea agglomerans -Pantoea deleyi -Pantoea dispersa -Pantoea sp. -Pantomorus postfasciatus -Panulirus argus -Panulirus echinatus -Panulirus homarus -Panulirus ornatus -Panurus biarmicus -Papaver atlanticum -Papaver bracteatum -Papaver nudicaule -Papaver pavoninum -Papaver rhoeas -Papaver somniferum -Papaveraceae -Paphia -Paphies subtriangulata -Paphiopedilum dianthum -Papilionidae -Papio -Papio anubis -Papio cynocephalus -Papio hamadryas -Papio hamadryas hamadryas -Papio kindae -Papio papio -Papio sp. -Papio ursinus -Parabacteroides -Parabacteroides distasonis -Parabacteroides faecis -Parabacteroides merdae -Parabuteo unicinctus -Paracidovorax cattleyae -Paracidovorax citrulli -Paracidovorax oryzae -Paracidovorax valerianellae -Paracoccaceae -Paracoccaceae bacterium -Paracoccus -Paracoccus kondratievae -Paracoccus marcusii -Paracoccus marginatus -Paracoccus sp. (in: a-proteobacteria) -Paracoccus sulfuroxidans -Paracoccus thiocyanatus -Paracoccus versutus -Paracoccus yeei -Paracyprichromis brieni -Paradoxurus -Paradoxurus hermaphroditus -Paradoxurus musangus -Paradoxurus zeylonensis -Parageobacillus thermoglucosidasius -Parageobacillus toebii -Paraglaciecola -Paraglomus brasilianum -Parahaemoproteus -Parahyaena brunnea -Parahypsugo crassulus -Paralichthys lethostigma -Paralichthys olivaceus -Parambassis ranga -Paramuricea placomus -Parapercis lutevittata -Parapercis pacifica -Parapercis sexfasciata -Parapoynx stagnalis -Parapristipoma trilineatum -Pararge aegeria -Pararheinheimera soli -Paraschema detectendum -Parascorpaena picta -Parasteatoda tepidariorum -Parastrellus hesperus -Parasynechococcus marenigrum WH 8102 -Paratemnopteryx couloniana -Paratrachymyrmex -Paratrachymyrmex diversus -Paratriaenops furculus -Pardalotus punctatus -Pareronia valeria -Pareuchaetes pseudoinsulata -Parietaria officinalis -Paris polyphylla -Paris polyphylla var. yunnanensis -Paris quadrifolia -Paris vietnamensis -Parkesia noveboracensis -Parkinsonia florida -Parnara guttata -Parodia leninghausii -Parthenium -Parthenium hysterophorus -Parthenocissus heterophylla -Parthenocissus tricuspidata -Parulidae -Parupeneus cyclostomus -Parus major -Parvipsitta porphyrocephala -Pasiphaea japonica -Pasiphila rectangulata -Paspalum -Paspalum conjugatum -Paspalum dilatatum -Paspalum distichum -Paspalum notatum -Paspalum setaceum -Paspalum thunbergii -Passer -Passer domesticus -Passer montanus -Passer sp. -Passerella iliaca -Passeridae -Passeriformes -Passerina cyanea -Passiflora -Passiflora alata -Passiflora auriculata -Passiflora caerulea -Passiflora cincinnata -Passiflora edulis -Passiflora edulis f. edulis -Passiflora edulis f. flavicarpa -Passiflora eichleriana x Passiflora gibertii -Passiflora foetida -Passiflora incarnata -Passiflora suberosa -Passiflora tarminiana -Pasteurella multocida -Pastinaca sativa -Patrinia scabiosifolia -Pavo -Pavo cristatus -Pavo muticus -Pavonia -Pecari tajacu -Pectinophora gossypiella -Pectobacterium -Pectobacterium aroidearum -Pectobacterium atrosepticum -Pectobacterium atrosepticum SCRI1043 -Pectobacterium brasiliense -Pectobacterium carotovorum -Pectobacterium carotovorum subsp. carotovorum -Pectobacterium odoriferum -Pectobacterium polaris -Pectobacterium sp. -Pectobacterium wasabiae -Pedalium murex -Pedilanthus -Pediococcus -Peganum harmala -Pekania pennanti -Pelargonium -Pelargonium peltatum -Pelargonium radula -Pelargonium x hortorum -Pelargonium zonale -Pelates quadrilineatus -Pelea capreolus -Pelecanidae -Pelecanus -Pelecanus conspicillatus -Pelecanus crispus -Pelecanus erythrorhynchos -Pelecanus occidentalis -Pelecanus philippensis -Pelecanus thagus -Pelecinus polyturator -Pelecus cultratus -Pellaea atropurpurea -Pellia neesiana -Pelobates fuscus -Pelodiscus sinensis -Pelomedusa -Pelomys isseli -Pelophylax chosenicus -Pelophylax lessonae -Pelophylax nigromaculatus -Pelophylax perezi -Pelophylax plancyi -Pelophylax ridibundus -Pelusios williamsi -Pempsamacra -Penaeidae -Penaeus -Penaeus californiensis -Penaeus chinensis -Penaeus duorarum -Penaeus esculentus x Penaeus monodon -Penaeus indicus -Penaeus japonicus -Penaeus latisulcatus -Penaeus merguiensis -Penaeus monodon -Penaeus penicillatus -Penaeus semisulcatus -Penaeus setiferus -Penaeus stylirostris -Penaeus vannamei -Penelope superciliaris -Penelopina nigra -Penicillidia conspicua -Penicillium adametzioides -Penicillium atramentosum -Penicillium aurantiogriseum -Penicillium brasilianum -Penicillium brevicompactum -Penicillium cairnsense -Penicillium camemberti -Penicillium chrysogenum -Penicillium citreosulfuratum -Penicillium citrinum -Penicillium digitatum -Penicillium glabrum -Penicillium italicum -Penicillium janczewskii -Penicillium janthinellum -Penicillium miczynskii -Penicillium olsonii -Penicillium raistrickii -Penicillium roqueforti -Penicillium roseopurpureum -Penicillium spinulosum -Penicillium stoloniferum -Penicillium sumatraense -Penicillium vanoranjei -Penicillium viridicatum -Penicillium waksmanii -Penstemon -Penstemon digitalis -Pentalonia nigronervosa -Pentaneurella katterjokki -Pentapodus -Pentapogon crinitus -Pentodon -Peperomia caperata -Peperomia marmorata -Peperomia obtusifolia -Peperomia tuisana -Peponocephala electra -Perameles bougainville -Perca -Perca flavescens -Perca fluviatilis -Percalates novemaculeata -Percidae -Percina -Percocypris pingi -Percopsis omiscomaycus -Perdicinae -Perdix perdix -Pereskiopsis kellermanii -Pergularia daemia -Pericallis -Pericallis hybrida -Periconia byssoides -Periconia macrospinosa -Peridroma -Peridroma saucia -Perigonia lusca -Perilampus aeneus -Perilla -Perilla frutescens -Perilla frutescens var. crispa -Perimyotis subflavus -Perina nuda -Perinereis aibuhitensis -Periophthalmodon schlosseri -Periparus ater -Periplaneta americana -Peripsocus phaeopterus -Perisesarma bidens -Peristrophe -Perla marginata -Peromyscus -Peromyscus attwateri -Peromyscus aztecus evides -Peromyscus beatae -Peromyscus boylii -Peromyscus boylii utahensis -Peromyscus californicus -Peromyscus crinitus -Peromyscus eremicus -Peromyscus hylocetes -Peromyscus leucopus -Peromyscus levipes -Peromyscus maniculatus -Peromyscus megalops -Peromyscus melanotis -Peromyscus mexicanus -Peromyscus ochraventer -Peromyscus pectoralis -Peromyscus sp. -Peromyscus spicilegus -Peromyscus truei -Peropteryx macrotis -Persea americana -Persea lingue -Persicaria minor -Peruphasma schultei -Pestalotiopsis fici -Pestalotiopsis mangiferae -Petasites japonicus -Petaurus breviceps -Petrochirus diogenes -Petrochromis famula -Petrochromis fasciolatus -Petrochromis macrognathus -Petrochromis polyodon -Petrogale godmani -Petroica australis -Petroica longipes -Petroica macrocephala -Petroica traversi -Petroselinum crispum -Petunia -Petunia exserta -Petunia sp. -Petunia x hybrida -Peyerimhoffina gracilis -Phacelia tanacetifolia -Phacochoerus aethiopicus -Phacochoerus africanus -Phaenicophaeus curvirostris -Phaeoacremonium minimum -Phaeobacter inhibens DSM 17395 -Phaeobotryon rhois -Phaeoceros carolinianus -Phaeocystis globosa -Phaeocystis pouchetii -Phaffia rhodozyma -Phagocata gracilis -Phagocata morgani -Phaius -Phaius tancarvilleae -Phakopsora pachyrhizi -Phakopsora pachyrhizi Thai1 -Phalacrocoracidae -Phalacrocorax -Phalacrocorax auritus -Phalacrocorax brasilianus -Phalacrocorax capensis -Phalacrocorax capillatus -Phalacrocorax carbo -Phalacrocorax pelagicus -Phalaenopsis -Phalaenopsis amabilis -Phalaenopsis equestris -Phalaenopsis pulcherrima -Phalaenopsis sp. -Phalaris aquatica -Phalaris canariensis -Phalaris coerulescens -Phalaris minor -Phalera bucephala -Phaps chalcoptera -Pharaxonotha floridana -Phascolarctos cinereus -Phaseolus -Phaseolus coccineus -Phaseolus leptostachyus -Phaseolus lunatus -Phaseolus vulgaris -Phasianidae -Phasianinae -Phasianus -Phasianus colchicus -Phasianus versicolor -Phasmatodea -Phelipanche aegyptiaca -Phelipanche ramosa -Phellodendron amurense -Phenacoccus solenopsis -Pheucticus melanocephalus -Philander opossum -Philantomba maxwellii -Philantomba monticola -Philesturnus carunculatus -Philoctetes bogdanovii -Philodendron -Philodromus dispar -Philotrypesis -Philotrypesis pilosa -Philydor erythrocercum -Phlebiopsis gigantea -Phlebotominae -Phlebotomus -Phlebotomus ariasi -Phlebotomus longicuspis -Phlebotomus major -Phlebotomus neglectus -Phlebotomus papatasi -Phlebotomus perfiliewi -Phlebotomus perniciosus -Phlebotomus sergenti -Phlebotomus tobbi -Phleum pratense -Phlox -Phlox carolina -Phlox divaricata -Phlox drummondii -Phlox glaberrima -Phlox hybrid cultivar -Phlox paniculata -Phlox pilosa -Phlox stolonifera -Phoca -Phoca fasciata -Phoca groenlandica -Phoca largha -Phoca vitulina -Phoca vitulina concolor -Phoca vitulina richardii -Phoca vitulina vitulina -Phocaeicola dorei -Phocaeicola dorei CL02T12C06 -Phocaeicola massiliensis -Phocaeicola vulgatus -Phocidae -Phocoena phocoena -Phocoena spinipinnis -Phocoenidae -Phodopus roborovskii -Phodopus sungorus -Phoebastria immutabilis -Phoeniconaias minor -Phoenicoparrus andinus -Phoenicopteridae -Phoenicopterus chilensis -Phoenicopterus roseus -Phoenicopterus ruber -Phoenicopterus ruber ruber -Phoenicopterus sp. -Phoeniculus purpureus -Phoenicurus auroreus -Phoenicurus phoenicurus -Phoenix dactylifera -Pholidota -Phomopsis -Phomopsis asparagi -Phoniscus -Phoridae -Phormidium -Phormidium sp. MIS-PhA -Photinia serratifolia -Photinus pyralis -Photobacterium damselae -Photopectoralis bindus -Phragmites australis -Phryganidia californica -Phryma leptostachya -Phrynocephalus erythrurus -Phrynocephalus theobaldi -Phthorimaea operculella -Phycocalidia -Phylidonyris novaehollandiae -Phyllanthus emblica -Phyllanthus niruri -Phyllanthus urinaria -Phylloscopus -Phylloscopus borealis -Phylloscopus collybita -Phylloscopus coronatus -Phylloscopus fuscatus -Phylloscopus inornatus -Phylloscopus proregulus -Phylloscopus schwarzi -Phylloscopus tenellipes -Phyllostachys aureosulcata -Phyllostachys aureosulcata f. spectabilis -Phyllostachys bambusoides -Phyllostachys edulis -Phyllostachys nigra -Phyllostachys parvifolia -Phyllostachys prominens -Phyllostachys rubromarginata -Phyllostachys yunhoensis -Phyllosticta citriasiana -Phyllostomus discolor -Phyllostomus elongatus -Phyllostomus hastatus -Phymateus viridipes -Physalis -Physalis angulata -Physalis divaricata -Physalis heterophylla -Physalis ixocarpa -Physalis minima -Physalis peruviana -Physalis philadelphica -Physalis pubescens -Physarum polycephalum -Physcomitrium patens -Physeter catodon -Physiculus japonicus -Physostegia -Phytolacca acinosa -Phytolacca americana -Phytophthora cactorum -Phytophthora castaneae -Phytophthora condilina -Phytophthora fragariae -Phytophthora heveae -Phytophthora infestans -Phytophthora parasitica -Phytophthora pluvialis -Phytophthora sp. -Piaya minuta -Pica -Pica hudsonia -Pica nuttalli -Pica pica -Picea rubens -Pichia membranifaciens -Picidae -Picoa juniperi -Picoides villosus -Picrorhiza kurrooa -Picus canus -Pieris brassicae -Pieris rapae -Piliocolobus badius -Piliocolobus badius badius -Piliocolobus badius temminckii -Piliocolobus rufomitratus -Piliocolobus tephrosceles -Piliocolobus tholloni -Pimephales promelas -Pimoa altioculata -Pinctada fucata -Pinellia pedatisecta -Pinellia ternata -Pinellia tripartita -Pinguicula agnata -Pinicola enucleator -Pinus albicaulis -Pinus flexilis -Pinus nigra -Pinus patula -Pinus sylvestris -Pionites -Pionites leucogaster -Pionites melanocephalus -Pionus chalcopterus -Pionus fuscus -Pionus maximiliani -Pionus menstruus -Pionus menstruus reichenowi -Piper -Piper argyrophyllum -Piper attenuatum -Piper barberi -Piper betle -Piper colubrinum -Piper cubeba -Piper galeatum -Piper longum -Piper methysticum -Piper mullesua -Piper nigrum -Piper ornatum -Piper peepuloides -Piper retrofractum -Piper sarmentosum -Piper sp. 'bababudani' -Piper thomsonii -Piper trichostachyon -Piperaceae -Pipistrellus -Pipistrellus abramus -Pipistrellus coromandra -Pipistrellus hesperidus -Pipistrellus inexspectatus -Pipistrellus kuhlii -Pipistrellus musciculus -Pipistrellus nanulus -Pipistrellus nathusii -Pipistrellus pipistrellus -Pipistrellus pygmaeus -Pipistrellus sp. pipistrellus/pygmaeus AO-2021 -Pipistrellys abramus -Piranga ludoviciana -Pisaster ochraceus -Pistacia chinensis -Pistacia lentiscus -Pistacia terebinthus -Pistacia vera -Pisum sativum -Pisum sativum var. arvense -Pisum sativum var. macrocarpum -Pitangus sulphuratus -Pithecia pithecia -Pithecia pithecia pithecia -Pithomyces chartarum -Pittosporum -Pittosporum tobira -Pituophis catenifer -Pituophis melanoleucus -Pityohyphantes rubrofasciatus -Plagiomnium insigne -Plagiopsetta -Planaria torva -Planctomycetes bacterium ZRK32 -Planiliza affinis -Planiliza tade -Planktothrix agardhii -Planktothrix agardhii HAB637 -Planococcus citri -Planococcus ficus -Planotaenium ohtanii -Plantago -Plantago asiatica -Plantago depressa -Plantago lagopus -Plantago lanceolata -Plantago major -Plantago media -Plasmodium vivax -Plasmopara halstedii -Plasmopara viticola -Platalea minor -Platanistidae -Platax orbicularis -Platichthys flesus -Platichthys stellatus -Platnickina tincta -Platycephalus indicus -Platycephalus richardsoni -Platycercus -Platycercus elegans -Platycercus eximius -Platycercus icterotis -Platycercus venustus -Platycladus orientalis -Platycodon grandiflorus -Platyrhina -Platyrrhini -Platyrrhinus lineatus -Plautia stali -Plea minutissima -Plecoglossus altivelis -Plecotus auritus -Plecotus austriacus -Plecotus gaisleri -Plecotus sacrimontis -Plectonema -Plectonema sp. -Plectranthus aromaticus -Plectrophenax nivalis -Plectropomus leopardus -Plectropterus gambensis -Plegadis falcinellus -Pleione formosana -Pleione humilis -Plenodomus biglobosus -Pleospora typhicola -Pleosporaceae sp. -Pleosporales -Plesiomonas shigelloides -Plesiomonas sp. -Plethodon cinereus -Pleurobema sintoxia -Pleurochrysis sp. (in: haptophytes) -Pleuromamma abdominalis -Pleuronectes platessa -Pleuronectiformes -Pleuronichthys japonicus -Pleurosicya -Pleurotus ostreatus -Ploceus cucullatus -Ploceus melanocephalus -Ploceus ocularis -Ploceus vitellinus -Plodia interpunctella -Plumeria -Plumeria obtusa -Plumeria pudica -Plumeria rubra -Plumeria x stenopetala -Plutella xylostella -Pluvialis apricaria -Pluvialis fulva -Pluvialis squatarola -Pneumolaelaps longanalis -Poa anceps -Poa annua -Poa cita -Poa cookii -Poa persica -Poa pratensis -Poa trivialis -Poaceae -Podagrion pachymerum -Podarcis filfolensis -Podarcis siculus -Podargus strigoides -Podiceps cristatus -Podiceps grisegena -Podicipediformes -Podosphaera prunicola -Podosphaera tridactyla -Podosphaera xanthii -Podranea ricasoliana -Poecile -Poecile atricapillus -Poecile carolinensis -Poecile montanus -Poecile palustris -Poecilia latipinna -Poecilia reticulata -Poecilia sphenops -Poephila acuticauda -Poephila personata -Pogona barbata -Pogona minor -Pogona vitticeps -Pogostemon cablin -Poicephalus cryptoxanthus -Poicephalus gulielmi -Poicephalus gulielmi massaicus -Poicephalus meyeri -Poicephalus robustus -Poicephalus rueppellii -Poicephalus rufiventris -Poicephalus senegalus -Poicephalus sp. -Polaribacter -Polaribacter sp. AHE13PA -Polaribacter sp. HaHaR_3_91 -Polaribacter sp. R2A056_3_33 -Polaromonas sp. -Polioptila caerulea -Polistes chinensis -Polistes dominula -Polistes metricus -Polistes nimpha -Polistes sp. -Pollachius virens -Polyblepharides amylifera -Polycarpa mytiligera -Polycarpon tetraphyllum -Polycelis nigra -Polydesmidae -Polygala garcinii -Polygonatum cyrtonema -Polygonatum kingianum -Polygonum -Polygonum cuspidatum -Polypedates megacephalus -Polyphaga aegyptiaca -Polyplectron malacense -Polypogon monspeliensis -Polyscias -Polyscias balfouriana -Polyscias fruticosa -Polysticta stelleri -Polytelis anthopeplus -Polytelis swainsonii -Pomacanthus imperator -Pomacanthus maculosus -Pomacanthus xanthometopon -Pomacea canaliculata -Pomacentrus moluccensis -Pomatoschistus minutus -Pombalia attenuata -Pompilus cinereus -Pongamia pinnata -Pongo -Pongo abelii -Pongo pygmaeus -Pongo pygmaeus pygmaeus -Pontederia vaginalis -Pontimonas salivibrio -Pontoporia blainvillei -Populus alba -Populus alba var. pyramidalis -Populus sp. -Populus tomentosa -Populus tremula -Populus x canadensis -Porcellio scaber -Porcellio siculoccidentalis -Porcula salvania -Porifera -Porites sp. -Poropanchax normani -Porphyridium purpureum -Porphyrio martinica -Portulaca -Portulaca grandiflora -Portulaca molokiniensis -Portulaca oleracea -Portulaca pilosa -Portunus pelagicus -Portunus trituberculatus -Potamochoerus larvatus -Potamochoerus porcus -Potamopyrgus antipodarum -Potentilla pindicola -Potos flavus -Pouzolzia hirta -Pouzolzia zeylanica -Powellomyces hirtus -Praomys -Praomys derooi -Praomys jacksoni -Praomys misonnei -Praomys mutoni -Praomys petteri -Praomys rostratus -Praomys tullbergi -Prasiola crispa -Pratia pedunculata -Pratylenchus penetrans -Premna serratifolia -Presbytis melalophos -Prescottella equi -Prevotella -Prevotella ruminicola -Prevotella sp. -Priacanthus macracanthus -Priestia megaterium -Priestia megaterium DSM 319 -Primates -Primnoa pacifica -Primolius auricollis -Primolius couloni -Primolius maracana -Primula -Primula malacoides -Primula obconica -Priodontes maximus -Prionailurus bengalensis -Prionailurus bengalensis euptilurus -Prionailurus viverrinus -Prionodon linsang -Pristiapogon exostigma -Pristipomoides sieboldii -Probopyrinella latreuticola -Proboscidea louisiana -Probosciger aterrimus -Procambarus clarkii -Procapra gutturosa -Procapra przewalskii -Procarduelis nipalensis -Procavia capensis -Prochlorococcus -Prochlorococcus marinus -Prochlorococcus marinus str. MIT 9215 -Prochlorococcus marinus str. MIT 9303 -Prochlorococcus marinus str. MIT 9312 -Prochlorococcus marinus str. MIT 9313 -Prochlorococcus marinus str. NATL2A -Prochlorococcus marinus subsp. marinus str. CCMP1375 -Prochlorococcus marinus subsp. pastoris str. CCMP1986 -Procolobus verus -Procordulia grayi -Procotyla fluviatilis -Procyon -Procyon cancrivorus -Procyon lotor -Proechimys cuvieri -Proechimys guyannensis -Proechimys semispinosus -Proechimys sp. -Progne subis -Promerops cafer -Propionibacterium -Propionibacterium freudenreichii -Propionibacterium freudenreichii subsp. shermanii -Propithecus coquereli -Propithecus diadema -Prorocentrum cf. balticum -Prorocentrum lima -Proscyllium habereri -Prostheceraeus vittatus -Protaetiibacter -Proteles cristata -Proteus -Proteus mirabilis -Proteus penneri -Proteus sp. (in: enterobacteria) -Proteus vulgaris -Protobothrops mucrosquamatus -Protopterus annectens -Providencia -Providencia rettgeri -Providencia sp. -Providencia stuartii -Prunella modularis -Prunella montanella -Prunus -Prunus armeniaca -Prunus avium -Prunus bokhariensis -Prunus brigantina -Prunus caroliniana -Prunus cerasifera -Prunus cerasifera x Prunus munsoniana -Prunus cerasoides -Prunus cerasus -Prunus davidiana -Prunus domestica -Prunus domestica subsp. insititia -Prunus dulcis -Prunus emarginata -Prunus fruticosa -Prunus glandulosa -Prunus humilis -Prunus incisa -Prunus japonica -Prunus lusitanica -Prunus mahaleb -Prunus mume -Prunus nigra -Prunus persica -Prunus persica f. compressa -Prunus persica var. nucipersica -Prunus pseudocerasus -Prunus salicina -Prunus serotina -Prunus serrulata -Prunus simonii -Prunus spinosa -Prunus tomentosa -Prunus yedoensis -Prymnesiophyceae -Prymnesium kappa -Prymnesium parvum -Prymnesium polylepis -Psammolestes coreodes -Psammomys obesus -Psammotettix alienus -Psarocolius -Psathyromyia abonnenci -Psenopsis anomala -Psephotellus chrysopterygius -Psephotellus dissimilis -Psephotellus varius -Psephotus haematonotus -Pseudacris maculata -Pseudaeromonas pectinilytica -Pseudanabaena -Pseudanabaena sp. -Pseudanthias squamipinnis -Pseudapis diversipes -Pseudelephantopus spicatus -Pseudemys concinna concinna -Pseuderanthemum reticulatum -Pseudetroplus maculatus -Pseudo-nitzschia australis -Pseudo-nitzschia fraudulenta -Pseudo-nitzschia multiseries -Pseudoalteromonas -Pseudoalteromonas atlantica -Pseudoalteromonas marina -Pseudoalteromonas marina DSM 17587 -Pseudoalteromonas phenolica -Pseudoalteromonas sp. -Pseudoalteromonas sp. Bq0 -Pseudoalteromonas sp. H105 -Pseudoalteromonas sp. H6 -Pseudoalteromonas sp. YD6 -Pseudoanthidium scapulare -Pseudocaranx dentex -Pseudocercospora eumusae -Pseudochondrostoma polylepis -Pseudogymnoascus destructans -Pseudohemiculter dispar -Pseudois nayaur -Pseudomonadota -Pseudomonas -Pseudomonas aeruginosa -Pseudomonas aeruginosa ATCC 15442 -Pseudomonas aeruginosa CHA -Pseudomonas aeruginosa DSM 50071 = NBRC 12689 -Pseudomonas aeruginosa LESB58 -Pseudomonas aeruginosa PA1 -Pseudomonas aeruginosa PA14 -Pseudomonas aeruginosa PAK -Pseudomonas aeruginosa PAO1 -Pseudomonas aeruginosa UCBPP-PA14 -Pseudomonas agarici -Pseudomonas alcaligenes -Pseudomonas cannabina pv. alisalensis -Pseudomonas carnis -Pseudomonas chlororaphis -Pseudomonas cichorii -Pseudomonas cuatrocienegasensis -Pseudomonas fluorescens -Pseudomonas fluorescens group -Pseudomonas fluorescens Q8r1-96 -Pseudomonas fluorescens SBW25 -Pseudomonas grimontii -Pseudomonas koreensis -Pseudomonas lactis -Pseudomonas luteola -Pseudomonas oryzihabitans -Pseudomonas otitidis -Pseudomonas plecoglossicida -Pseudomonas protegens -Pseudomonas putida -Pseudomonas putida KT2440 -Pseudomonas putida NBRC 14164 -Pseudomonas putida S12 -Pseudomonas savastanoi -Pseudomonas savastanoi pv. glycinea -Pseudomonas savastanoi pv. phaseolicola -Pseudomonas sivasensis -Pseudomonas sp. -Pseudomonas sp. 1-1-1b -Pseudomonas sp. ANT_H14 -Pseudomonas sp. D3 -Pseudomonas syringae -Pseudomonas syringae pv. actinidiae -Pseudomonas syringae pv. actinidiae ICMP 18800 -Pseudomonas syringae pv. avii -Pseudomonas syringae pv. syringae -Pseudomonas syringae pv. tomato str. DC3000 -Pseudomonas tolaasii -Pseudomonas tolaasii NCPPB 2192 -Pseudopezicula -Pseudophycis -Pseudopleuronectes americanus -Pseudopleuronectes yokohamae -Pseudorasbora parva -Pseudorca crassidens -Pseudorhombus -Pseudorhombus arsius -Pseudorhombus cinnamoneus -Pseudosasa -Pseudosasa amabilis -Pseudosasa japonica -Pseudosasa usawae -Pseudoscops clamator -Pseudosimochromis babaulti -Pseudostellaria heterophylla -Pseudotsuga sinensis var. wilsoniana -Pseudoxanthomonas kaohsiungensis -Psilogramma increta -Psilotrema simillimum -Psittacara erythrogenys -Psittacara leucophthalmus -Psittacara wagleri -Psittacidae -Psittaciformes -Psittacula alexandri -Psittacula cyanocephala -Psittacula derbiana -Psittacula echo -Psittacula eques -Psittacula eupatria -Psittacula finschii -Psittacula himalayana -Psittacula krameri -Psittacula krameri manillensis -Psittacula sp. -Psittacus erithacus -Psittacus erithacus erithacus -Psittacus timneh -Psitteuteles goldiei -Psophocarpus tetragonolobus -Psorophora -Psorophora albigenu -Psorophora albipes -Psorophora ciliata -Psorophora cingulata -Psorophora columbiae -Psorophora confinnis -Psorophora ferox -Psorophora funiculus -Psorophora howardii -Psorophora varinervis -Psorophora varipes -Psoroptes ovis -Psychoda alternata -Psychodidae -Psychodopygus panamensis -Psychrobacillus -Psychrobacillus psychrodurans -Psychrobacter aquimaris -Psychrobacter sp. -Psychrobacter sp. MV2 -Psychrobacter sp. OW20 -Ptelea trifoliata -Ptenochirus jagorii -Pterapogon kauderni -Pteris vittata -Pterocles exustus -Pterodroma cookii -Pteroglossus viridis -Pterolocera amplicornis -Pteromalus puparum -Pteronotus alitonus -Pteronotus davyi -Pteronotus parnellii -Pteronotus rubiginosus -Pterophyllum scalare -Pteropodidae -Pteropus -Pteropus alecto -Pteropus conspicillatus -Pteropus giganteus -Pteropus hypomelanus -Pteropus lylei -Pteropus melanotus natalis -Pteropus poliocephalus -Pteropus rufus -Pteropus scapulatus -Pteropus sp. -Pteropus tonganus -Pteropus vampyrus -Pterostylis coccina -Pterostylis curta -Pterostylis nutans -Pterostylis sanguinea -Pterygotrigla hemisticta -Ptilidium ciliare var. pulcherrimum -Ptilonorhynchus violaceus -Ptilotula penicillata -Ptyas major -Ptychadena sp. -Puccinia helianthi -Puccinia striiformis -Puccinia striiformis f. sp. tritici -Pudu -Pudu puda -Pueraria montana -Pueraria montana var. lobata -Puma concolor -Puma concolor couguar -Puma yagouaroundi -Puncha ratzeburgi -Punica granatum -Puniceicoccales -Purpureicephalus spurius -Purpureocillium lilacinum -Pusa caspica -Pusa hispida -Pusa sibirica -Pycnococcus provasolii -Pycnonotidae -Pycnonotus jocosus -Pycnonotus leucotis -Pycnonotus sinensis -Pycnopodia helianthoides -Pygathrix nemaeus -Pygiopsylla -Pygocentrus nattereri -Pygoscelis -Pygoscelis adeliae -Pygoscelis antarcticus -Pygoscelis papua -Pyramimonas plurioculata -Pyrenacantha -Pyricularia grisea -Pyricularia oryzae -Pyriglena leucoptera -Pyrobaculum arsenaticum -Pyrobaculum sp. -Pyrobaculum sp. D11 -Pyrococcus abyssi -Pyroderus scutatus -Pyrodinium bahamense -Pyropia pseudolinearis -Pyrrhocorax graculus -Pyrrhocoris apterus -Pyrrhula erythaca -Pyrrhula pyrrhula -Pyrrhula pyrrhula griseiventris -Pyrrhura cruentata -Pyrrhura frontalis -Pyrrhura griseipectus -Pyrrhura molinae -Pyrrhura rhodocephala -Pyrus -Pyrus amygdaliformis -Pyrus betulifolia -Pyrus calleryana -Pyrus communis -Pyrus pashia -Pyrus pyraster -Pyrus pyrifolia -Pyrus x bretschneideri -Python -Python anchietae -Python bivittatus -Python breitensteini -Python brongersmai -Python curtus -Python molurus -Python regius -Pytilia hypogrammica -Pyxis arachnoides -Quartinia thebaica -Quasipaa spinosa -Quelea quelea -Quercus castanea -Quercus coccifera -Quercus marilandica -Quercus prinoides -Quercus robur -Quiscalus -Quiscalus major -Quiscalus mexicanus -Quiscalus quiscula -Rachiplusia nu -Rachycentron canadum -Rahnella woolbedingensis -Rallidae -Rallus aquaticus -Ralstonia -Ralstonia pickettii -Ralstonia pseudosolanacearum -Ralstonia solanacearum -Ralstonia solanacearum UW551 -Ramphastos -Ramphastos sp. -Ramphastos toco -Ramphocelus carbo -Rana aurora -Rana dalmatina -Rana dybowskii -Rana huanrensis -Rana iberica -Rana temporaria -Rangifer tarandus -Rangifer tarandus caribou -Rangifer tarandus granti -Rangifer tarandus tarandus -Ranitomeya ventrimaculata -Ranoidea caerulea -Ranoidea splendida -Ranunculus -Ranunculus arvensis -Ranunculus asiaticus -Ranunculus elegans -Ranunculus japonicus -Ranunculus sardous -Raoultella -Raoultella ornithinolytica -Raoultella planticola -Raphanus -Raphanus raphanistrum -Raphanus sativus -Raphanus sativus var. niger -Raphanus sativus var. sativus -Raphanus sp. -Raphicerus campestris -Rapistrum rugosum -Rathayibacter toxicus -Rattus -Rattus andamanensis -Rattus annandalei -Rattus argentiventer -Rattus cf. marmosurus TG-2020 -Rattus exulans -Rattus flavipectus -Rattus fuscipes -Rattus hoffmanni -Rattus losea -Rattus nitidus -Rattus norvegicus -Rattus pyctoris -Rattus rattus -Rattus rattus alexandrinus -Rattus sp. -Rattus sp. r3 YH-2020 -Rattus tanezumi -Rattus tanezumi sladeni -Rattus tiomanicus -Rattus xanthurus -Ratufa bicolor -Ratufa macroura -Rauvolfia serpentina -Recilia dorsalis -Recurvirostra novaehollandiae -Regina -Regulus satrapa -Rehmannia -Rehmannia glutinosa -Reinhardtius hippoglossoides -Reithrodontomys -Reithrodontomys creper -Reithrodontomys fulvescens -Reithrodontomys megalotis -Reithrodontomys mexicanus -Reithrodontomys sumichrasti -Renanthera -Retropinna retropinna -Retropinna semoni -Rexea solandri -Rhabdomys pumilio -Rhabdophis tigrinus -Rhagodia eremaea -Rhagovelia obesa -Rhamnus lycioides -Rhaphiolepis bibas -Rhea -Rheinheimera sp. BAL341 -Rheum -Rheum palmatum -Rheum rhabarbarum -Rheum rhaponticum -Rhinella marina -Rhinobatos hynnicephalus -Rhinoceros unicornis -Rhinolophidae -Rhinolophus -Rhinolophus acuminatus -Rhinolophus affinis -Rhinolophus alcyone -Rhinolophus blasii -Rhinolophus blythi -Rhinolophus capensis -Rhinolophus clivosus -Rhinolophus coelophyllus -Rhinolophus cornutus -Rhinolophus creaghi -Rhinolophus darlingi -Rhinolophus denti -Rhinolophus eloquens -Rhinolophus euryale -Rhinolophus ferrumequinum -Rhinolophus fumigatus -Rhinolophus hildebrandti -Rhinolophus hipposideros -Rhinolophus landeri -Rhinolophus lepidus -Rhinolophus lobatus -Rhinolophus luctus -Rhinolophus macrotis -Rhinolophus malayanus -Rhinolophus marshalli -Rhinolophus megaphyllus -Rhinolophus mehelyi -Rhinolophus monoceros -Rhinolophus pearsonii -Rhinolophus pusillus -Rhinolophus rex -Rhinolophus rhodesiae -Rhinolophus rouxii -Rhinolophus shameli -Rhinolophus siamensis -Rhinolophus simulator -Rhinolophus sinicus -Rhinolophus smithersi -Rhinolophus sp. CN 2016 -Rhinolophus stheno -Rhinolophus subbadius -Rhinolophus thomasi -Rhinolophus trifoliatus -Rhinonicteris aurantia -Rhinophylla pumilio -Rhinopithecus roxellana -Rhinopoma hardwickii -Rhinopomatidae -Rhinosciurus laticaudatus -Rhionaeschna multicolor -Rhipicephalus -Rhipicephalus annulatus -Rhipicephalus appendiculatus -Rhipicephalus bursa -Rhipicephalus decoloratus -Rhipicephalus evertsi evertsi -Rhipicephalus geigyi -Rhipicephalus guilhoni -Rhipicephalus haemaphysaloides -Rhipicephalus microplus -Rhipicephalus muhsamae -Rhipicephalus pulchellus -Rhipicephalus pumilio -Rhipicephalus sanguineus -Rhipicephalus sanguineus sensu lato -Rhipicephalus turanicus -Rhipidura albiscapa -Rhipidura fuliginosa -Rhizobium -Rhizobium etli -Rhizobium etli CFN 42 -Rhizobium etli GR56 -Rhizobium gallicum -Rhizobium leguminosarum -Rhizobium leguminosarum bv. trifolii -Rhizobium phaseoli -Rhizobium sp. N324 -Rhizobium sp. N4311 -Rhizobium sp. N941 -Rhizobium sp. R339 -Rhizobium sp. R635 -Rhizobium sp. R693 -Rhizochromulina -Rhizoctonia -Rhizoctonia fumigata -Rhizoctonia solani -Rhizoctonia solani AG-1 IA -Rhizoctonia solani AG-3 -Rhizoctonia solani AG-4 HGI -Rhizoctonia solani AG-4 HGIII -Rhizoctonia sp. -Rhizomys -Rhizomys pruinosus -Rhizomys sinensis -Rhizophagus -Rhizophagus clarus -Rhizophagus irregularis -Rhizophagus irregularis DAOM 197198w -Rhizophagus sp. HR1 -Rhizopus arrhizus -Rhizopus microsporus -Rhizopus stolonifer -Rhodactis indosinensis -Rhodella violacea -Rhodiola rosea -Rhodnius neglectus -Rhodnius prolixus -Rhodobacter -Rhodobacter capsulatus SB 1003 -Rhodobacter capsulatus YW1 -Rhodochaete parvula -Rhodococcus -Rhodococcus erythropolis -Rhodococcus globerulus -Rhodococcus opacus -Rhodococcus rhodochrous -Rhododendron delavayi -Rhododendron maximum -Rhodoferax lacus -Rhodophyta -Rhodosorus marinus -Rhodosporidiobolus odoratus -Rhodothermus -Rhodothermus marinus -Rhodovulum -Rhodovulum sp. P5 -Rhogeessa tumida -Rhombomys opimus -Rhopalosiphum maidis -Rhopalosiphum padi -Rhynchobatus djiddensis -Rhynchonycteris naso -Rhynchophorus ferrugineus -Rhynchosia -Rhynchosia capitata -Rhynchosia minima -Rhynchotus rufescens -Rhyzopertha dominica -Ribes -Ribes alpinum -Ribes americanum -Ribes aureum -Ribes fasciculatum var. chinense -Ribes fragrans -Ribes nigrum -Ribes petraeum -Ribes rubrum -Ribes spicatum -Ribes uva-crispa -Richardia scabra -Ricinus communis -Riemerella anatipestifer -Rieppeleon brevicaudatus -Riparia paludicola -Riptortus pedestris -Rissa tridactyla -Rita -Rivina humilis -Robinia -Robinia pseudoacacia -Rodentia -Rodentia sp. -Romalea microptera -Rorippa indica -Rorippa islandica -Rorippa palustris -Rosa -Rosa brunonii -Rosa chinensis -Rosa hybrid cultivar -Rosa lucieae -Rosa multiflora -Rosa rubiginosa -Rosa rugosa -Rosa sp. -Rosa x alba -Rosa x damascena -Rosa x fortuneana -Rosaceae -Roseburia intestinalis L1-82 -Rosellinia necatrix -Roseobacter -Roseobacter denitrificans -Roseobacter denitrificans OCh 114 -Roseovarius nubinhibens -Roseovarius sp. 217 -Rotheca serrata -Rothia dentocariosa -Rottboellia -Rottboellia cochinchinensis -Rousettus -Rousettus aegyptiacus -Rousettus amplexicaudatus -Rousettus leschenaultii -Rousettus madagascariensis -Rousettus sp. -Roystonea regia -Rubus -Rubus canadensis -Rubus clinocephalus -Rubus coreanus -Rubus discolor -Rubus ellipticus -Rubus glaucus -Rubus hirsutus -Rubus idaeus -Rubus occidentalis -Rubus plicatus -Rubus praecox -Rubus sp. sect. Rubus (R. fruticosus agg.) -Rubus ursinus -Rudbeckia -Rudbeckia hirta -Rudbeckia hirta var. pulcherrima -Ruditapes philippinarum -Ruegeria -Ruegeria pomeroyi -Ruegeria pomeroyi DSS-3 -Ruegeria sp. AU67 -Ruellia -Ruellia blechum -Ruellia humilis -Rugonectria rugulosa -Rumex -Rumex acetosa -Rumex crispus -Rumex dentatus -Rumex hastatus -Rumex hypogaeus -Rumex nepalensis -Rumex obtusifolius -Rumex patientia -Ruminantia -Rumohra adiantiformis -Rupicapra pyrenaica -Rupicapra rupicapra -Rupicapra rupicapra rupicapra -Rupornis magnirostris -Rusa -Rusa alfredi -Rusa timorensis -Rusa unicolor -Rusa unicolor swinhoei -Rutilus rutilus -Rutstroemia firma -Ruwenzorisorex suncoides -Rynchops niger -Sabethes -Sabethes albiprivus -Sabethes belisarioi -Sabethes chloropterus -Sabethes glaucodaemon -Sabethes gymnothorax -Sabethes intermedius -Saccharina latissima -Saccharolobus shibatae -Saccharolobus solfataricus -Saccharolobus solfataricus P2 -Saccharomonospora sp. -Saccharomyces cerevisiae -Saccharomyces cerevisiae YJM1199 -Saccharomyces kudriavzevii -Saccharomyces paradoxus -Saccharomyces uvarum -Saccharum -Saccharum barberi -Saccharum hybrid cultivar -Saccharum hybrid cultivar BO91 -Saccharum hybrid cultivar Co 1148 -Saccharum hybrid cultivar Co 419 -Saccharum hybrid cultivar Co 740 -Saccharum hybrid cultivar Co 86032 -Saccharum hybrid cultivar Co 93009 -Saccharum hybrid cultivar Co 94008 -Saccharum hybrid cultivar Co 99006 -Saccharum hybrid cultivar CoC 671 -Saccharum hybrid cultivar CoS 767 -Saccharum hybrid cultivar CP65-357 -Saccharum hybrid cultivar CP72-1210 -Saccharum hybrid cultivar FN15 -Saccharum hybrid cultivar GT11 -Saccharum hybrid cultivar H32-8560 -Saccharum hybrid cultivar H50-7209 -Saccharum hybrid cultivar H87-4094 -Saccharum hybrid cultivar NCo 376 -Saccharum hybrid cultivar R570 -Saccharum hybrid cultivar ROC16 -Saccharum hybrid cultivar ROC22 -Saccharum officinarum -Saccharum robustum -Saccharum rufipilum -Saccharum sinense -Saccharum sp. -Saccharum spontaneum -Saccolaimus flaviventris -Saccolaimus saccolaimus -Saccopteryx bilineata -Saccostomus sp. -Sagittaria pygmaea -Sagittaria trifolia -Saguinus -Saguinus bicolor -Saguinus imperator -Saguinus labiatus -Saguinus midas -Saguinus mystax -Saguinus oedipus -Saiga -Saiga tatarica mongolica -Saimiri -Saimiri boliviensis -Saimiri boliviensis boliviensis -Saimiri boliviensis peruviensis -Saimiri sciureus -Saimiri sciureus albigena -Saimiri sciureus macrodon -Saimiri sciureus sciureus -Saimiri sp. -Saimiri ustus -Salamandra salamandra -Salarias guttatus -Salariopsis fluviatilis -Salicola -Salicola sp. PV4 -Salicornia perennis -Salinibacter -Salinibacter ruber -Salinibacter ruber M8 -Salinivibrio costicola -Salinivibrio sp. -Salipiger abyssi -Salipiger profundus -Salisaeta sp. SP9-1 -Salix atrocinerea -Salix dasyclados -Salmo carpio -Salmo macrostigma -Salmo marmoratus -Salmo salar -Salmo trutta -Salmo trutta fario -Salmo trutta trutta -Salmonella -Salmonella enterica -Salmonella enterica subsp. enterica -Salmonella enterica subsp. enterica serovar Albany -Salmonella enterica subsp. enterica serovar Anatum -Salmonella enterica subsp. enterica serovar Braenderup -Salmonella enterica subsp. enterica serovar Brandenburg -Salmonella enterica subsp. enterica serovar Enteritidis -Salmonella enterica subsp. enterica serovar Enteritidis str. LK5 -Salmonella enterica subsp. enterica serovar Gallinarum -Salmonella enterica subsp. enterica serovar Hadar -Salmonella enterica subsp. enterica serovar Heidelberg -Salmonella enterica subsp. enterica serovar Infantis -Salmonella enterica subsp. enterica serovar Javiana -Salmonella enterica subsp. enterica serovar Kentucky -Salmonella enterica subsp. enterica serovar Newlands -Salmonella enterica subsp. enterica serovar Newport -Salmonella enterica subsp. enterica serovar Paratyphi A -Salmonella enterica subsp. enterica serovar Paratyphi B -Salmonella enterica subsp. enterica serovar Pullorum -Salmonella enterica subsp. enterica serovar Rissen -Salmonella enterica subsp. enterica serovar Saintpaul -Salmonella enterica subsp. enterica serovar Sendai -Salmonella enterica subsp. enterica serovar Shubra -Salmonella enterica subsp. enterica serovar Thompson -Salmonella enterica subsp. enterica serovar Typhi -Salmonella enterica subsp. enterica serovar Typhimurium -Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 -Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 -Salmonella sp. -Salmonella sp. S7 -Salmonidae -Salmoninae -Saltator maximus -Salticidae -Salvelinus -Salvelinus alpinus -Salvelinus fontinalis -Salvelinus namaycush -Salvia -Salvia azurea var. grandiflora -Salvia divinorum -Salvia dorisiana -Salvia hispanica -Salvia miltiorrhiza -Salvia plebeia -Salvia rosmarinus -Salvia sclarea -Salvia splendens -Salvia subgen. Rosmarinus -Samanea saman -Sambucus -Sambucus canadensis -Sambucus nigra -Sambucus racemosa -Sambucus racemosa subsp. kamtschatica -Samia cynthia -Samia ricini -Sandalus niger -Sander lucioperca -Sander vitreus -Sandersonia aurantiaca -Sanguinaria canadensis -Sanicula chinensis -Sapajus -Sapajus apella -Sapajus libidinosus -Sapajus nigritus -Sapajus nigritus robustus -Sapajus sp. -Sapajus xanthosternos -Sapindus mukorossi -Sarcochilus hartmannii -Sarcophaga impatiens -Sarcophaga melanura -Sarcophaga sp. -Sarcophilus harrisii -Sarcoptes scabiei -Sarcosphaera coronaria -Sarda australis -Sarda orientalis -Sardina pilchardus -Sardinella -Sardinella aurita -Sardinella lemuru -Sardinella longiceps -Sardinops caeruleus -Sardinops sagax -Sargassum thunbergii -Sargocentron ittodai -Sarkidiornis sylvicola -Sarpa salpa -Sarracenia -Satureja -Saurida lessepsianus -Saurida undosquamis -Sauropus androgynus -Saussurea lyrata -Saxicola torquatus -Scadoxus multiflorus -Scadoxus puniceus -Scaeva pyrastri -Scaevola calliptera -Scalopus aquaticus -Scandix pecten-veneris -Scandosorbus intermedia -Scapania nemorea -Scaphiophryne madagascariensis -Scaphirhynchus albus -Scaphoideus titanus -Scaptodrosophila deflexa -Scaptonyx fusicaudus -Scaptotrigona postica -Scarus rubroviolaceus -Scatella stagnalis -Scathophaga furcata -Scathophaga stercoraria -Scatophagidae -Sceliphron caementarium -Schaalia odontolytica -Schedorhinotermes intermedius -Scheffersomyces segobiensis -Schefflera -Schisandra chinensis -Schistocephalus solidus -Schistosoma japonicum -Schistosoma mansoni -Schistosoma turkestanicum -Schistosomatidae -Schizothorax waltoni -Schlumbergera -Schlumbergera truncata -Schmidtea mediterranea -Sciaenops ocellatus -Scirpophaga incertulas -Scirtothrips dorsalis -Sciuridae -Sciurotamias davidianus -Sciurus carolinensis -Sciurus niger -Sciurus vulgaris -Sclerochloa dura -Scleropages formosus -Sclerophthora macrospora -Sclerostachya -Sclerotinia minor -Sclerotinia nivalis -Sclerotinia sclerotiorum -Sclerotium hydrophilum -Scoliodon macrorhynchos -Scolopacidae -Scolopax rusticola -Scolopterus penicillatus -Scolytinae -Scomber japonicus -Scomber scombrus -Scophthalmus maximus -Scopolia -Scopolia japonica -Scorpaena jacksoniensis -Scorpaena scrofa -Scorpiurus muricatus -Scortum barcoo -Scoterepens balstoni -Scotinomys xerampelinus -Scotinophara lurida -Scotoecus -Scotophilus -Scotophilus dinganii -Scotophilus heathii -Scotophilus kuhlii -Scotophilus leucogaster -Scotophilus nux -Scrophularia buergeriana -Scrophularia nodosa -Scutellaria baicalensis -Scutellospora calospora -Scutigera coleoptrata -Scylla -Scylla paramamosain -Scylla serrata -Sea -Sebastes melanops -Sebastes mentella -Sebastes nigrocinctus -Sebastes schlegelii -Secale cereale -Securigera varia -Sedum -Sedum sarmentosum -Seemannia gymnostoma -Seemannia nematanthodes -Seemannia purpurascens -Segestria pacifica -Seiurus aurocapilla -Seladonia subaurata -Selaginella kraussiana -Selaginella wallacei -Selenicereus costaricensis -Selenicereus megalanthus -Selenicereus monacanthus -Selenicereus stenopterus -Selenicereus trigonus -Selenicereus undatus -Selenomonas ruminantium -Semiarundinaria densiflora -Semiarundinaria fastuosa -Semnopithecus entellus -Senecio scandens -Senecio vulgaris -Senna -Senna alata -Senna bicapsularis -Senna hirsuta -Senna latifolia -Senna macranthera -Senna multiglandulosa -Senna obtusifolia -Senna occidentalis -Senna rizzinii -Senna septemtrionalis -Senna tora -Senna uniflora -Sepedon violaceus -Sergentomyia -Sergentomyia khawi -Sergentomyia minuta -Serinus canaria -Serinus leucopygius -Seriola dumerili -Seriola quinqueradiata -Serpentes -Serranidae -Serranus cabrilla -Serratia -Serratia fonticola -Serratia liquefaciens -Serratia marcescens -Serratia rubidaea -Serratia sp. (in: enterobacteria) -Serratia sp. ATCC 39006 -Serratia sp. OS31 -Sesamia inferens -Sesamum -Sesamum indicum -Sesarmidae -Sesbania -Sesbania bispinosa -Setaria adhaerens -Setaria barbata -Setaria faberi -Setaria grisebachii -Setaria italica -Setaria pumila -Setaria verticillata -Setaria viridis -Setonix brachyurus -Setophaga auduboni -Setophaga coronata -Setophaga petechia -Setophaga petechia aureola -Setophaga striata -Setothosea asigna -Shewanella -Shewanella baltica -Shewanella fidelis -Shewanella indica -Shewanella inventionis -Shewanella oneidensis -Shewanella oneidensis MR-1 -Shewanella putrefaciens -Shewanella sp. -Shewanella sp. M16 -Shigella -Shigella boydii -Shigella dysenteriae -Shigella flexneri -Shigella flexneri 1c -Shigella flexneri 2a -Shigella sonnei -Shigella sp. -Shimwellia blattae -Sialia -Sialis lutaria -Sibirionetta formosa -Sicana odorifera -Sicyoidochytrium minutum -Sicyonia brevirostris -Sicyonia sp. Fukuoka2019 -Sicyos angulatus -Sicyos australis -Sicyos edulis -Sida -Sida acuta -Sida aggregata -Sida ciliaris -Sida collina -Sida cordata -Sida cordifolia -Sida haenkeana -Sida rhombifolia -Sida spinosa -Sida urens -Sidastrum -Sidastrum micranthum -Siganus canaliculatus -Siganus luridus -Sigesbeckia glabrescens -Sigesbeckia orientalis -Sigmodon -Sigmodon alstoni -Sigmodon arizonae -Sigmodon hispidus -Sigmodon mascotensis -Sigmoidotropis elegans -Silene cognata -Silene dioica -Silene latifolia -Silene subgen. Lychnis -Sillago ciliata -Sillago flindersi -Sillago sihama -Siluridae -Siluriformes -Silurus glanis -Silurus soldatovi -Silvanigrella aquatica -Silybum marianum -Simiiformes -Simitidion simile -Simochromis diagramma -Simosyrphus grandicornis -Simplicillium sympodiophorum -Simulium -Simulium aureohirtum -Simulium meridionale -Simulium sp. -Sinapis alba -Sinapis arvensis -Sinibotia superciliaris -Siniperca chuatsi -Siniperca scherzeri -Sinningia speciosa -Sinobambusa tootsik -Sinomenium acutum -Sinomonas atrocyanea -Sinonovacula constricta -Sinorhizobium americanum -Sinorhizobium meliloti -Sinorhizobium meliloti 1021 -Sinorhizobium meliloti 2011 -Sinorhizobium sp. LM21 -Siphonaptera -Sipuncula -Siraitia grosvenorii -Sisymbrium -Sisymbrium irio -Sisymbrium loeselii -Sisymbrium officinale -Sisymbrium orientale -Sisyrinchium atlanticum -Sitobion avenae -Sitobion miscanthi -Sitophilus zeamais -Sitta canadensis -Sitta europaea -Skeletonema costatum -Skermania piniformis -Smallanthus sonchifolius -Smilax auriculata -Smilax china -Sodalis glossinidius -Sodalis glossinidius str. 'morsitans' -Sodiomyces alkalinus -Sogatella furcifera -Solanaceae -Solanum -Solanum acaule -Solanum aculeatissimum -Solanum aethiopicum -Solanum americanum -Solanum anguivi -Solanum betaceum -Solanum capsicastrum -Solanum carolinense -Solanum chacoense -Solanum chancayense -Solanum chaucha -Solanum chenopodioides -Solanum coagulans -Solanum dasyphyllum -Solanum dimidiatum -Solanum dulcamara -Solanum elaeagnifolium -Solanum gourlayi -Solanum habrochaites -Solanum hyporhodium -Solanum jamaicense -Solanum lasiocarpum -Solanum lasiophyllum -Solanum laxum -Solanum lichtensteinii -Solanum lycopersicum -Solanum lycopersicum var. cerasiforme -Solanum lyratum -Solanum macrocarpon -Solanum mammosum -Solanum mauritianum -Solanum melongena -Solanum microdontum -Solanum muricatum -Solanum nigrescens -Solanum nigrum -Solanum nodiflorum -Solanum palinacanthum -Solanum palustre -Solanum panduriforme -Solanum paniculatum -Solanum pennellii -Solanum peruvianum -Solanum phureja -Solanum pimpinellifolium -Solanum pseudocapsicum -Solanum pseudolulo -Solanum quitoense -Solanum retroflexum -Solanum rostratum -Solanum scabrum -Solanum scuticum -Solanum sessiliflorum -Solanum sisymbriifolium -Solanum stenotomum subsp. goniocalyx -Solanum stoloniferum -Solanum stramoniifolium -Solanum subinerme -Solanum torvum -Solanum tuberosum -Solanum tuberosum subsp. andigenum -Solanum velleum -Solanum viarum -Solanum villosum -Solanum violifolium -Solanum virginianum -Solanum x curtilobum -Solanum x juzepczukii -Solea -Solea senegalensis -Solea solea -Soleidae -Solenopsis geminata -Solenopsis invicta -Solenopsis richteri -Solenostemon -Solidago canadensis -Solobacterium moorei -Somateria fischeri -Somateria mollissima -Somateria spectabilis -Somatochlora meridionalis -Sonchus -Sonchus arvensis -Sonchus asper -Sonchus megalocarpus -Sonchus oleraceus -Sonchus tenerrimus -Sophora alopecuroides -Sophora microphylla -Sorbaria sorbifolia -Sorbus -Sorbus aucuparia -Sorbus glomerulata -Sorbus pteridophylla -Sorbus rehderiana -Sorbus scalaris -Sorex -Sorex araneus -Sorex bairdi -Sorex bedfordiae -Sorex caecutiens -Sorex cinereus -Sorex coronatus -Sorex cylindricauda -Sorex daphaenodon -Sorex fumeus -Sorex haydeni -Sorex hoyi -Sorex isodon -Sorex minutissimus -Sorex minutus -Sorex mirabilis -Sorex monticolus -Sorex palustris -Sorex roboratus -Sorex trowbridgii -Sorex tundrensis -Sorex unguiculatus -Sorex vagrans -Sorghastrum nutans -Sorghum -Sorghum arundinaceum -Sorghum bicolor -Sorghum halepense -Sorghum hybrid cultivar -Sorghum x almum -Soricidae -Soricidae sp. YH-2020 -Sotalia guianensis -Sousa chinensis -Spalangia cameroni -Sparidae -Spartina -Sparus aurata -Spathiphyllum -Spathiphyllum patinii -Spathoglottis -Spathomorpha lancettifer -Spatula clypeata -Spatula discors -Spatula platalea -Spatula querquedula -Speothos venaticus -Spermacoce articularis -Spermacoce latifolia -Spermatophyta -Spermophilus dauricus -Spermophilus erythrogenys -Sphaeridiotrema pseudoglobulus -Sphaerium novaezelandiae -Sphaerophoria -Sphaerophoria scripta -Sphaerotilus natans -Sphagnum palustre -Sphecodes albilabris -Spheniscidae -Spheniscus demersus -Spheniscus humboldti -Spheniscus magellanicus -Sphenodon -Sphenodon punctatus -Sphenostylis stenocarpa -Sphictostethus nitidus -Sphingobium sp. IP1 -Sphingomonas -Sphingomonas paucimobilis -Sphingomonas sp. LR55 -Sphingomonas turrisvirgatae -Sphingopyxis sp. -Sphyraena japonica -Sphyraena sphyraena -Sphyrna lewini -Spicara smaris -Spigelia anthelmia -Spilarctia lutea -Spilarctia obliqua -Spilogale -Spilogale putorius -Spilomena beata -Spilopelia chinensis -Spilopelia senegalensis -Spilopsyllus cuniculi -Spilornis cheela -Spinacia oleracea -Spinacia tetrandra -Spinturnicidae -Spinulum annotinum -Spinus atratus -Spinus cucullatus -Spinus pinus -Spinus psaltria -Spinus spinus -Spinus tristis -Spiraea sp. -Spiralizoros caudelli -Spiranthes cernua -Spiroplasma -Spiroplasma citri -Spiroplasma kunkelii -Spiroplasma poulsonii -Spissistilus festinus -Spodoptera albula -Spodoptera cosmioides -Spodoptera eridania -Spodoptera exempta -Spodoptera exigua -Spodoptera frugiperda -Spodoptera littoralis -Spodoptera litura -Spondyliosoma cantharus -Sporobolus -Sporophila angolensis -Sporormiaceae sp. -Sporosarcina aquimarina -Sprattus -Sprattus sprattus -Sprattus sprattus sprattus -Spuriopimpinella brachycarpa -Squalius cephalus -Squalus brevirostris -Stachys affinis -Stachys byzantina -Stachytarpheta -Stachytarpheta jamaicensis -Staehelina dubia -Stagonosporopsis cucurbitacearum -Staphylococcus -Staphylococcus arlettae -Staphylococcus aureus -Staphylococcus aureus HIP07256 -Staphylococcus aureus subsp. aureus N315 -Staphylococcus aureus subsp. aureus NCTC 8325 -Staphylococcus aureus subsp. aureus PS187 -Staphylococcus aureus subsp. aureus RN4220 -Staphylococcus aureus subsp. aureus str. Newman -Staphylococcus capitis -Staphylococcus caprae -Staphylococcus carnosus -Staphylococcus cohnii -Staphylococcus epidermidis -Staphylococcus epidermidis 36-1 -Staphylococcus epidermidis RP62A -Staphylococcus equorum -Staphylococcus haemolyticus -Staphylococcus hominis -Staphylococcus hyicus -Staphylococcus pasteuri -Staphylococcus pseudintermedius -Staphylococcus pseudintermedius E140 -Staphylococcus pseudintermedius ED99 -Staphylococcus saprophyticus -Staphylococcus sp. -Staphylococcus succinus -Staphylococcus ureilyticus -Staphylococcus warneri -Staphylococcus xylosus -Stappia indica -Starmerella bacillaris -Staurastrum sebaldii -Steatoda capensis -Steatoda grossa -Steatomys pratensis -Steatomys sp. -Steganacarus carinatus -Steganacarus magnus -Stegastes partitus -Steinernema ceratophorum -Stelis breviuscula -Stellaria media -Stemodia jorullensis -Stemphylium lycopersici -Stemphylium solani -Stenella coeruleoalba -Stenella frontalis -Stenella longirostris -Steno bredanensis -Stenocephalemys -Stenocephalemys albipes -Stenodermatinae -Stenomesson -Stenoscepa -Stenotaphrum secundatum -Stenotrophomonas -Stenotrophomonas maltophilia -Stenotrophomonas sp. -Stephanocircus -Stephanotis volubilis -Stercorarius lonnbergi -Stercorarius maccormicki -Sterna -Sterna dougallii -Sterna hirundinacea -Sterna hirundo -Sternbergia lutea -Sternula -Sternula albifrons -Sternula antillarum -Stethorus sp. -Stevia -Stevia rebaudiana -Stigmochelys pardalis -Stipagrostis -Stizoptera bichenovii -Stokesia -Stomatopoda -Stomoxys calcitrans -Streblidae -Streptobotrys caulophylli -Streptocarpus -Streptocarpus ionanthus -Streptocarpus sect. Saintpaulia -Streptocarpus x hybridus -Streptococcus -Streptococcus acidominimus -Streptococcus agalactiae -Streptococcus agalactiae 09mas018883 -Streptococcus agalactiae A909 -Streptococcus agalactiae BSU248 -Streptococcus agalactiae BSU450 -Streptococcus agalactiae BSU451 -Streptococcus agalactiae CCUG 17336 -Streptococcus agalactiae CCUG 30636 -Streptococcus agalactiae CCUG 37736 -Streptococcus agalactiae CCUG 39096 A -Streptococcus agalactiae GB00082 -Streptococcus agalactiae GB00111 -Streptococcus agalactiae GB00640 -Streptococcus agalactiae GB00901 -Streptococcus agalactiae GD201008-001 -Streptococcus agalactiae ILRI005 -Streptococcus agalactiae SGBS026 -Streptococcus agalactiae SGBS029 -Streptococcus anginosus -Streptococcus anginosus 1_2_62CV -Streptococcus anginosus 1505 -Streptococcus anginosus C238 -Streptococcus anginosus DORA_7 -Streptococcus anginosus F0211 -Streptococcus anginosus MAS624 -Streptococcus anginosus SK1138 -Streptococcus anginosus subsp. whileyi CCUG 39159 -Streptococcus azizii -Streptococcus caballi DSM 19004 -Streptococcus canis -Streptococcus canis FSL Z3-227 -Streptococcus castoreus DSM 17536 -Streptococcus constellatus -Streptococcus cristatus -Streptococcus cristatus AS 1.3089 -Streptococcus cuniculi -Streptococcus dysgalactiae -Streptococcus entericus DSM 14446 -Streptococcus equi -Streptococcus equinus -Streptococcus equinus 2B -Streptococcus equinus JB1 -Streptococcus gallolyticus -Streptococcus gallolyticus UCN34 -Streptococcus gordonii -Streptococcus halotolerans -Streptococcus henryi -Streptococcus henryi DSM 19005 -Streptococcus himalayensis -Streptococcus hyovaginalis DSM 12219 -Streptococcus ictaluri 707-05 -Streptococcus infantarius -Streptococcus infantis -Streptococcus infantis SK970 -Streptococcus iniae -Streptococcus iniae SF1 -Streptococcus intermedius -Streptococcus intermedius F0413 -Streptococcus intermedius JTH08 -Streptococcus intermedius SK54 = ATCC 27335 -Streptococcus lutetiensis -Streptococcus macedonicus -Streptococcus marmotae -Streptococcus merionis DSM 19192 -Streptococcus mitis -Streptococcus mitis B6 -Streptococcus mitis SK1080 -Streptococcus mitis SK321 -Streptococcus mitis SK564 -Streptococcus mitis SK569 -Streptococcus mitis SK575 -Streptococcus mitis SK616 -Streptococcus mutans -Streptococcus oralis -Streptococcus oralis ATCC 49296 -Streptococcus oralis SK304 -Streptococcus oralis SK313 -Streptococcus orisratti DSM 15617 -Streptococcus parasanguinis -Streptococcus parasanguinis ATCC 15912 -Streptococcus parasanguinis CC87K -Streptococcus parasanguinis F0449 -Streptococcus parauberis -Streptococcus parauberis KCTC 11537 -Streptococcus parauberis KCTC 11980BP -Streptococcus parauberis KRS-02083 -Streptococcus parauberis KRS-02109 -Streptococcus parauberis NCFD 2020 -Streptococcus pasteurianus -Streptococcus phocae -Streptococcus phocae subsp. salmonis -Streptococcus plurextorum DSM 22810 -Streptococcus pneumoniae -Streptococcus pneumoniae 23F -Streptococcus pneumoniae 670-6B -Streptococcus pneumoniae 70585 -Streptococcus pneumoniae AP200 -Streptococcus pneumoniae BS458 -Streptococcus pneumoniae D39 -Streptococcus pneumoniae GA07228 -Streptococcus pneumoniae GA13637 -Streptococcus pneumoniae GA16121 -Streptococcus pneumoniae GA17328 -Streptococcus pneumoniae GA41317 -Streptococcus pneumoniae GA41538 -Streptococcus pneumoniae GA47033 -Streptococcus pneumoniae GA47373 -Streptococcus pneumoniae GA47502 -Streptococcus pneumoniae R6 -Streptococcus pneumoniae SP6-BS73 -Streptococcus pneumoniae ST556 -Streptococcus porci DSM 23759 -Streptococcus porcinus -Streptococcus porcinus str. Jelinkova 176 -Streptococcus pseudopneumoniae -Streptococcus pseudopneumoniae 22725 -Streptococcus pseudopneumoniae 5247 -Streptococcus pseudopneumoniae ATCC BAA-960 = CCUG 49455 -Streptococcus pseudopneumoniae IS7493 -Streptococcus pseudoporcinus -Streptococcus pseudoporcinus LQ 940-04 -Streptococcus pseudoporcinus SPIN 20026 -Streptococcus pyogenes -Streptococcus pyogenes Alab49 -Streptococcus pyogenes GA03799 -Streptococcus pyogenes HSC5 -Streptococcus pyogenes M1 GAS -Streptococcus pyogenes MGAS10394 -Streptococcus pyogenes MGAS10750 -Streptococcus pyogenes MGAS2096 -Streptococcus pyogenes MGAS315 -Streptococcus pyogenes MGAS5005 -Streptococcus pyogenes MGAS6180 -Streptococcus pyogenes MGAS8232 -Streptococcus pyogenes MGAS9429 -Streptococcus pyogenes NZ131 -Streptococcus pyogenes SSI-1 -Streptococcus pyogenes str. Manfredo -Streptococcus salivarius -Streptococcus salivarius 57.I -Streptococcus salivarius JIM8777 -Streptococcus salivarius K12 -Streptococcus sanguinis -Streptococcus sanguinis SK1056 -Streptococcus sanguinis SK160 -Streptococcus sp. -Streptococcus suis -Streptococcus suis 05ZYH33 -Streptococcus suis 89-3576-3 -Streptococcus suis 89/1591 -Streptococcus suis 98HAH33 -Streptococcus suis A7 -Streptococcus suis BM407 -Streptococcus suis D12 -Streptococcus suis SS12 -Streptococcus suis ST1 -Streptococcus suis ST3 -Streptococcus suis T15 -Streptococcus suis TL13 -Streptococcus suis YB51 -Streptococcus suis YS39 -Streptococcus suis YS49 -Streptococcus thermophilus -Streptococcus thermophilus 1F8CT -Streptococcus thermophilus ASCC 1275 -Streptococcus thermophilus CNRZ1066 -Streptococcus thermophilus DGCC 7710 -Streptococcus thermophilus DSM 20617 -Streptococcus thermophilus LMD-9 -Streptococcus thermophilus MN-ZLW-002 -Streptococcus thermophilus ND03 -Streptococcus thermophilus TH1435 -Streptococcus thermophilus TH1477 -Streptococcus thoraltensis DSM 12221 -Streptococcus uberis -Streptococcus uberis 0140J -Streptococcus uberis 6736 -Streptococcus uberis 6780 -Streptococcus uberis Ab71 -Streptococcus uberis B190 -Streptococcus uberis B362 -Streptococcus uberis C5072 -Streptococcus uberis C5388 -Streptococcus uberis C8329 -Streptococcus uberis C9359 -Streptococcus uberis S6261 -Streptococcus urinalis -Streptococcus urinalis 2285-97 -Streptococcus urinalis FB127-CNA-2 -Streptococcus vestibularis -Streptococcus vestibularis ATCC 49124 -Streptococcus vestibularis F0396 -Streptolirion volubile -Streptomyces -Streptomyces avermitilis -Streptomyces azureus -Streptomyces coelicolor -Streptomyces coelicolor A3(2) -Streptomyces flavovirens -Streptomyces griseofuscus -Streptomyces griseus -Streptomyces indigocolor -Streptomyces lividans -Streptomyces mirabilis -Streptomyces platensis -Streptomyces rimosus -Streptomyces sanglieri -Streptomyces scabiei -Streptomyces sp. -Streptomyces sp. ZL12 -Streptomyces toxytricini -Streptomyces tricolor -Streptomyces venezuelae -Streptomyces venezuelae ATCC 10712 -Streptomyces virginiae -Streptomyces viridochromogenes -Streptomyces xanthochromogenes -Streptopelia -Streptopelia capicola -Streptopelia decaocto -Streptopelia orientalis -Streptopelia orientalis orii -Streptopelia turtur -Streptopus amplexifolius -Streptosolen jamesonii -Striga hermonthica -Strigidae -Strix aluco -Strix nebulosa -Strix nebulosa lapponica -Strix uralensis -Strix varia -Strongylocentrotus droebachiensis -Strongylocentrotus purpuratus -Strongylodon macrobotrys -Struthio -Struthio camelus -Struthioniformes -Sturnia pagodarum -Sturnidae -Sturnira -Sturnira angeli -Sturnira erythromos -Sturnira lilium -Sturnira ludovici -Sturnira tildae -Sturnus cineraceus -Sturnus sericeus -Sturnus vulgaris -Stutzerimonas stutzeri -Stylochus ellipticus -Stylommatophora -Stylophora pistillata -Stylops melittae -Stylosanthes -Stylosanthes guianensis -Styphnolobium japonicum -Styrax officinalis -Suaeda aegyptiaca -Suaeda fruticosa -Suaeda salsa -Sucra jujuba -Suidae -Suillus luteus -Sula dactylatra -Sula leucogaster -Sula sula -Sulfitobacter -Sulfitobacter sp. CB2047 -Sulfitobacter sp. EE-36 -Sulfitobacter sp. HGT1 -Sulfolobales -Sulfolobus -Sulfolobus beitou -Sulfolobus islandicus -Sulfolobus islandicus LAL14/1 -Sulfolobus sp. -Sulfolobus sp. A20 -Sulfolobus sp. E11-6 -Sulfolobus sp. G4ST-2 -Sulfolobus sp. G4ST-T-11 -Sulfolobus sp. G4T-1 -Sulfolobus tengchongensis -Suncus murinus -Sundamys infraluteus -Sundamys muelleri -Sundasciurus hippurus -Supella longipalpa -Suricata suricatta -Surnia ulula -Sus -Sus barbatus -Sus barbatus barbatus -Sus barbatus oi -Sus celebensis -Sus scrofa -Sus scrofa cristatus -Sus scrofa domesticus -Sus scrofa ibericus -Sus scrofa leucomystax -Sus scrofa scrofa -Sus sp. -Sus verrucosus -Sutcliffiella cohnii -Sutcliffiella halmapala -Sutera -Sutera cordata -Swertia japonica -Swinglea glutinosa -Syconycteris australis -Sycoscapter -Sylvia atricapilla -Sylvicapra grimmia -Sylvilagus audubonii -Sylvilagus bachmani -Sylvilagus floridanus -Sylvilagus sp. -Sylvirana guentheri -Sylvisorex -Symbiodinium -Symbiodinium sp. -Symmetrischema tangolias -Symmorphus murarius -Symphalangus syndactylus -Symphodus melops -Symphodus tinca -Symphysodon discus -Syncephalastrum racemosum -Syncerus caffer -Synchytrium microbalum -Synechococcus -Synechococcus elongatus PCC 7942 = FACHB-805 -Synechococcus sp. -Synechococcus sp. BL107 -Synechococcus sp. CB0101 -Synechococcus sp. CB0201 -Synechococcus sp. CB0202 -Synechococcus sp. CB0204 -Synechococcus sp. CB0208 -Synechococcus sp. CBW1002 -Synechococcus sp. CC9605 -Synechococcus sp. CC9902 -Synechococcus sp. KFM001 -Synechococcus sp. MIT S9220 -Synechococcus sp. MW02 -Synechococcus sp. PCC 7002 -Synechococcus sp. RCC307 -Synechococcus sp. SR-C1 -Synechococcus sp. TCC793 -Synechococcus sp. WH 6501 -Synechococcus sp. WH 7803 -Synechococcus sp. WH 7805 -Synechococcus sp. WH 8007 -Synechococcus sp. WH 8012 -Synechococcus sp. WH 8017 -Synechococcus sp. WH 8018 -Synechococcus sp. WH 8101 -Synechococcus sp. WH 8109 -Synedrella -Synedrella nodiflora -Synergus umbraculus -Syngnathus scovelli -Syngnathus typhle -Synodus macrops -Syntheosciurus granatensis -Syntrichia princeps -Syringa -Syringa oblata -Syringa vulgaris -Syrmaticus ellioti -Syrmaticus reevesii -Syrphus -Syrphus ribesii -Syrrhaptes paradoxus -Systropha curvicornis -Syzygium aromaticum -Tabanidae -Tabanus -Tabanus rufidens -Tabernaemontana divaricata -Tacca leontopetaloides -Tachybaptus ruficollis -Tachycixius pilosus -Tachyeres -Tachyglossus aculeatus -Tachysurus fulvidraco -Tadarida -Tadarida aegyptiaca -Tadarida brasiliensis -Tadarida brasiliensis mexicana -Tadarida teniotis -Tadorna -Tadorna ferruginea -Tadorna radjah -Tadorna tadorna -Tadorna tadornoides -Tadorna variegata -Taenia hydatigena -Taenia pisiformis -Taeniopygia guttata -Taeromys dominator -Tagetes -Tagetes erecta -Tagetes patula -Tagetes tenuifolia -Tagosodes orizicolus -Takhtajaniantha austriaca -Takifugu rubripes -Takydromus sexlineatus -Takydromus wolteri -Talaromyces amestolkiae -Talaromyces marneffei -Talaromyces neofusisporus -Talicada nyseus -Talipariti tiliaceum -Talpa altaica -Talpa aquitania -Talpa europaea -Talpa occidentalis -Tamandua tetradactyla -Tamias minimus -Tamias sibiricus -Tamias striatus -Tamiasciurus hudsonicus -Tamiops swinhoei -Tanacetum parthenium -Tangara mexicana -Tanichthys albonubes -Tanygnathus lucionensis -Taphozous longimanus -Taphozous mauritianus -Taphozous melanopogon -Taphozous perforatus -Taphozous sp. -Taphozous theobaldi -Tapinoma melanocephalum -Tapiridae -Tapirus -Taraxacum kok-saghyz -Taraxacum officinale -Taraxacum sp. -Tarentola mauritanica -Tarsiger cyanurus -Tarucus nara -Tatera -Taxidea taxus -Tecia solanivora -Tecoma stans -Tecomaria capensis -Tectona grandis -Tegillarca granosa -Teia anartoides -Telfairia occidentalis -Telmatochromis dhonti -Telmatochromis temporalis -Telosma cordata -Telosma odoratissima -Tenacibaculum geojense -Tenacibaculum maritimum -Tenacibaculum sp. -Tenacibaculum sp. AHE14PA -Tenebrio molitor -Tenebrionidae -Tenericutes bacterium zrk29 -Tengella perfuga -Tenodera sinensis -Tephrosia purpurea -Tephrosia senna -Terapon theraps -Teratoscincus roborowskii -Terfezia claveryi -Terminalia catappa -Termitogeton planus -Termitoidae -Terrapene -Terrapene carolina -Terrapene carolina carolina -Terrapene carolina triunguis -Terrapene ornata -Testudines -Testudinidae -Testudo -Testudo graeca -Testudo hermanni -Testudo horsfieldii -Testudo kleinmanni -Testudo marginata -Tetracerus quadricornis -Tetragenococcus halophilus -Tetragnatha maxillosa -Tetragnatha nitens -Tetragonia tetragonoides -Tetragonula carbonaria -Tetranychus urticae -Tetraponera penzigi -Tetraselmis chuii -Tetraselmis sp. -Tetraselmis viridis -Tetrasphaera jenkinsii -Tetrastes bonasia -Tetrastichus brontispae -Tetrix subulata -Tetrodontophora bielanensis -Tetronarce californica -Teucrium botrys -Teucrium fruticans -Thalassarche chlororhynchos -Thalassarche melanophris -Thalasseus elegans -Thalasseus maximus -Thalasseus sandvicensis -Thalassia testudinum -Thalassionema nitzschioides -Thalassiosira antarctica -Thalassiothrix antarctica -Thalassotalea loyana -Thaleichthys pacificus -Thalia dealbata -Thamnaconus septentrionalis -Thamnaconus striatus -Thamnophis saurita -Thaptomys nigrita -Thaumatotibia leucotreta -Thaumetopoea pityocampa -Thectocercus acuticaudatus -Thelebolus microsporus -Thelephora terrestris -Thelonectria sp. -Theobroma cacao -Theretra japonica -Therioaphis trifolii -Thermoanaerobacterium -Thermoanaerobacterium saccharolyticum JW/SL-YS485 -Thermobifida fusca -Thermococcus prieurii -Thermocrinis -Thermocrinis sp. -Thermoproteus sp. CP80 -Thermoproteus tenax -Thermus -Thermus scotoductus -Thermus sp. -Thermus sp. TC4 -Thermus thermophilus -Thermus thermophilus HB27 -Thermus thermophilus HB8 -Theropithecus gelada -Thesium chinense -Thevetia ahouai -Thevetia neriifolia -Thinornis novaeseelandiae -Thiohalocapsa -Thladiantha dubia -Thlaspi arvense -Tholymis tillarga -Thoopterus -Thoopterus nigrescens -Thoracica -Thraupis cyanocephala -Thraupis episcopus -Threskiornis aethiopicus -Threskiornis molucca -Threskiornithidae -Thrips palmi -Thrips tabaci -Thryomanes bewickii -Thryonomys gregorianus -Thryonomys sp. -Thryonomys swinderianus -Thryothorus ludovicianus -Thryssa dussumieri -Thunbergia -Thunbergia alata -Thunbergia erecta -Thunnus orientalis -Thunnus thynnus -Thymallus thymallus -Thyreus orbatus -Thyrinteina arnobia -Thyrsopteris elegans -Thysanoplusia orichalcea -Thysanoptera -Tibouchina -Tidestromia suffruticosa var. oblongifolia -Tigridia -Tigriopus californicus -Tilapia -Tilapia sp. -Tilia cordata -Tilia x europaea -Tiliqua rugosa -Tiliqua scincoides -Tinca tinca -Tineola bisselliella -Tipula oleracea -Tipula scripta -Titanodula formosana -Todiramphus cinnamominus -Todiramphus sanctus -Tolypocladium cylindrosporum -Tolypocladium ophioglossoides -Toona sinensis -Torenia anagallis -Torenia sp. -Torilis arvensis subsp. arvensis -Torilis japonica -Torilis sp. -Torulaspora delbrueckii -Toxocara -Toxoneuron nigriceps -Toxorhynchites splendens -Toxostoma rufum -Trabala vishnou -Trachelospermum asiaticum -Trachemys scripta elegans -Trachemys scripta scripta -Trachinotus blochii -Trachinotus carolinus -Trachinotus ovatus -Trachops cirrhosus -Trachurus -Trachurus japonicus -Trachurus mediterraneus -Trachurus novaezelandiae -Trachurus trachurus -Trachycephalus resinifictrix -Trachymyrmex intermedius -Trachypenaeus curvirostris -Trachypithecus cristatus -Trachypithecus francoisi -Trachypithecus pileatus -Trachysalambria curvirostris -Trachyspermum ammi -Tradescantia -Tradescantia fluminensis -Tradescantia spathacea -Tradescantia x andersoniana -Tradescantia zebrina -Tragelaphus -Tragelaphus angasii -Tragelaphus eurycerus -Tragelaphus imberbis -Tragelaphus oryx -Tragelaphus spekii -Tragelaphus strepsiceros -Tragopan caboti -Tragopogon -Tragopogon porrifolius -Tragulus javanicus -Tramea lacerata -Tranosema rostrale -Trapa natans -Traubia modesta -Trematocara marginatum -Trematocara nigrifrons -Trematomus bernacchii -Trematomus pennellii -Tremex magus -Treponema denticola ATCC 35405 -Tretanorhinus variabilis -Triacanthodes anomalus -Triaenophorus nodulosus -Triaenops afer -Triaenops menamena -Triaenops persicus -Trialeurodes vaporariorum -Triatoma delpontei -Triatoma infestans -Tribolium castaneum -Tribolium uniolae -Tribulus terrestris -Trichechus inunguis -Trichechus manatus -Trichechus manatus latirostris -Trichechus manatus manatus -Trichiurus lepturus -Trichobilharzia regenti -Trichobius sp. -Trichobius yunkeri -Trichocera saltator -Trichoderma asperellum -Trichoderma atroviride -Trichoderma citrinoviride -Trichoderma gamsii -Trichoderma hamatum -Trichoderma harzianum -Trichoderma koningiopsis -Trichoderma polysporum -Trichoderma reesei -Trichoderma rossicum -Trichoderma sp. -Trichoderma spirale -Trichoderma tomentosum -Trichoderma viride -Trichodes apiarius -Trichogaster -Trichogaster labiosa -Trichogaster lalius -Trichoglossus chlorolepidotus -Trichoglossus haematodus -Trichoglossus moluccanus -Trichoglossus rubritorquis -Trichomonas vaginalis -Trichonephila clavipes -Trichoniscus panormidensis -Trichopilia -Trichoplax sp. H2 -Trichoplusia ni -Trichopodus leerii -Trichopodus trichopterus -Trichopria drosophilae -Trichoprosopon -Trichoprosopon digitatum -Trichoprosopon theobaldi -Trichormus variabilis -Trichosanthes anguina -Trichosanthes cucumerina -Trichosanthes cucumeroides -Trichosanthes dioica -Trichosanthes kirilowii -Trichosurus vulpecula -Triclaria malachitacea -Tricyrtis formosana var. stolonifera -Tridax -Tridax procumbens -Trifolium -Trifolium alexandrinum -Trifolium campestre -Trifolium dubium -Trifolium fragiferum -Trifolium hybridum -Trifolium incarnatum -Trifolium pratense -Trifolium repens -Trifolium resupinatum -Trifolium subterraneum -Trifolium tembense -Trifolium vesiculosum -Trigonella -Trigonella foenum-graecum -Trillium chloropetalum -Trillium erectum -Trillium govanianum -Trillium grandiflorum -Trillium kurabayashii -Trillium ludovicianum -Trillium luteum -Trillium maculatum -Trillium recurvatum -Trillium stamineum -Trillium vaseyi -Trillium viridescens -Trimeresurus flavomaculatus -Trimeresurus hageni -Trimeresurus macrops -Trimma fangi -Trimma okinawae -Trimma striatum -Tringa glareola -Tringa nebularia -Tringa semipalmata -Tringa totanus -Trioceros -Trioceros jacksonii -Trioceros melleri -Triodia sylvina -Triparma pacifica -Tripidium arundinaceum -Tripidium ravennae -Tripleurospermum inodorum -Triplophysa siluroides -Tripterygium wilfordii -Trisetum flavescens -Trisopterus esmarkii -Trisopterus minutus -Triteleia -Triticum -Triticum aestivum -Triticum dicoccoides -Triticum monococcum subsp. aegilopoides -Triticum polonicum -Triticum sp. -Triticum spelta -Triticum turgidum -Triticum turgidum subsp. durum -Tritonibacter mobilis -Triturus marmoratus -Triumfetta -Trogonophis wiegmanni -Troides aeacus -Trombiculidae sp. -Tropaeolum majus -Tropaeolum tuberosum -Tropidophorus sinicus -Tropilaelaps clareae -Tropilaelaps mercedesae -Trueperella pyogenes -Tryonicus parvus -Trypoxylus dichotomus -Tscherskia triton -Tsukamurella inchonensis -Tsukamurella paurometabola -Tuber aestivum -Tulasnella -Tulasnella sp. -Tulbaghia violacea -Tulipa -Tulipa fosteriana -Tulipa gesneriana -Tulipa hybrid cultivar -Tunicata -Tupaia -Tupaia belangeri -Tupaia chinensis -Tupaia glis -Turdidae -Turdus hortulorum -Turdus iliacus -Turdus libonyana -Turdus merula -Turdus migratorius -Turdus naumanni -Turdus pallidus -Turdus philomelos -Turdus pilaris -Turdus rufiventris -Turdus serranus -Turritellidae -Tursiops -Tursiops aduncus -Tursiops truncatus -Tuta absoluta -Tylonycteris pachypus -Tylonycteris robustula -Tympanuchus cupido attwateri -Tympanuchus cupido pinnatus -Typhlomys cinereus -Typhonium -Typhonium flagelliforme -Typhonium trilobatum -Tyrophagus putrescentiae -Tyto alba -Uleiota planata -Ullucus tuberosus -Ulmus americana -Ulmus carpinifolia -Ulmus glabra -Ulmus laevis -Ulva australis -Ulva fenestrata -Ulva lactuca -Umbelopsis angularis -Umbelopsis dimorpha -Umbelopsis gibberispora -Umbelopsis ramanniana -Umbelopsis sp. -Umbelopsis versiformis -Umbilicaria phaea -Umbrina cirrosa -unclassified Phlebotomus -uncultured archaeon -Undaria pinnatifida -unidentified -unidentified bird -unidentified plant -Upeneichthys vlamingii -Upeneus japonicus -Upeneus moluccensis -Upeneus sulphureus -Upeneus tragula -Upupa epops -Upupidae -Uraeginthus bengalus -Uranomys ruddi -Uranotaenia -Uranotaenia chorleyi -Uranotaenia lowii -Uranotaenia mashonaensis -Uranotaenia sapphirina -Uranotaenia unguiculata -Uraria crinita -Urbanus proteus -Urena lobata -Uria -Uria aalge -Uria lomvia -Urochloa -Urochloa bovonei -Urochloa brizantha -Urochloa decumbens -Urochloa deflexa -Urochloa humidicola -Urochloa hybrida -Urochloa jubata -Urochloa lata -Urochloa mosambicensis -Urochloa nigropedata -Urochloa plantaginea -Urochloa platyphylla -Urochloa ruziziensis -Urochloa serrata -Urocissa erythroryncha -Urocitellus parryii -Urocitellus richardsonii -Urocitellus undulatus -Urocyon cinereoargenteus -Uroderma bilobatum -Urolophus aurantiacus -Uromyces appendiculatus -Uroplatus fimbriatus -Uropsilus sp. -Urospermum picroides -Urotrichus talpoides -Ursus americanus -Ursus americanus americanus -Ursus arctos -Ursus arctos arctos -Ursus arctos horribilis -Ursus arctos syriacus -Ursus maritimus -Ursus sp. -Ursus thibetanus -Ursus thibetanus laniger -Urtica -Urtica dioica -Urtica incisa -Urtica membranacea -Urtica urens -Urva auropunctata -Urva edwardsii -Urva javanica -Usnea chaetophora -Ustilaginoidea virens -Ustilago maydis -Utetheisa pulchella -Utricularia -Vaccinium -Vaccinium arctostaphylos -Vaccinium ashei -Vaccinium corymbosum -Vaccinium darrowii -Vaccinium macrocarpon -Vaccinium myrtillus -Valeriana -Valeriana fauriei -Valeriana jatamansi -Valerianella locusta -Valsa cypri -Valsa malicola -Vampyrodes caraccioli -Vanda -Vanda cristata -Vanellus chilensis -Vanellus spinosus -Vanellus vanellus -Vanessa atalanta -Vanessa cardui -Vanilla -Vanilla bahiana -Vanilla madagascariensis -Vanilla planifolia -Vanilla x tahitensis -Varanus albigularis -Varanus komodoensis -Varanus prasinus -Varecia variegata -Vargula hilgendorfii -Variabilichromis moorii -Variovorax -Variovorax sp. ZS18.2.2 -Varroa -Varroa destructor -Varroa jacobsoni -Varroa sp. -Varroa underwoodi -Vasconcellea cauliflora -Vasconcellea cundinamarcensis -Vasconcellea x heilbornii -Vaucheria litorea -Velarifictorus micado -Veltheimia bracteata -Verasper moseri -Verbascum -Verbena -Verbena canadensis -Verbena officinalis -Verbenaceae -Verbesina -Verbesina encelioides -Vermamoeba sp. -Vermamoeba vermiformis -Vernonia baldwinii -Veronica -Veronica bollonsii -Veronica breviracemosa -Veronica dieffenbachii -Veronica gentianoides -Veronica hybrid cultivar -Veronica persica -Veronica syriaca -Verrallina -Verrallina butleri -Verrallina funerea -Vertebrata -Verticillium albo-atrum -Verticillium dahliae -Verticillium longisporum -Vespa -Vespa affinis -Vespa crabro -Vespa mandarinia -Vespa simillima xanthoptera -Vespa velutina -Vespa velutina nigrithorax -Vespadelus baverstocki -Vespertilio murinus -Vespertilio sinensis -Vespertilionidae -Vespidae -Vespidae sp. -Vespoidea -Vespula -Vespula germanica -Vespula pensylvanica -Vespula vulgaris -Vestiaria coccinea -Vibrio -Vibrio alginolyticus -Vibrio alginolyticus NBRC 15630 = ATCC 17749 -Vibrio anguillarum -Vibrio breoganii -Vibrio campbellii -Vibrio campbellii ATCC BAA-1116 -Vibrio campbellii HY01 -Vibrio cholerae -Vibrio cholerae B33 -Vibrio cholerae O1 -Vibrio cholerae O1 biovar El Tor -Vibrio cholerae O139 -Vibrio cholerae O395 -Vibrio coralliilyticus -Vibrio coralliilyticus P1 -Vibrio crassostreae -Vibrio cyclitrophicus -Vibrio diazotrophicus -Vibrio hangzhouensis -Vibrio harveyi -Vibrio kanaloae -Vibrio lentus -Vibrio maritimus -Vibrio mediterranei -Vibrio metschnikovii -Vibrio mimicus -Vibrio natriegens -Vibrio neocaledonicus -Vibrio ordalii -Vibrio owensii -Vibrio parahaemolyticus -Vibrio pelagius -Vibrio rotiferianus -Vibrio rumoiensis -Vibrio sagamiensis -Vibrio sp. -Vibrio sp. 12A10 -Vibrio sp. 12G05 -Vibrio sp. F12 -Vibrio sp. F13 -Vibrio sp. LL003.15 -Vibrio sp. MV-5 -Vibrio sp. St2 -Vibrio sp. YD21 -Vibrio sp. YD38 -Vibrio splendidus -Vibrio tasmaniensis -Vibrio tubiashii -Vibrio variabilis -Vibrio vulnificus -Viburnum -Viburnum lentago -Viburnum tinus -Vicia cracca -Vicia ervilia -Vicia faba -Vicia sativa -Vicia sepium -Victoria -Vicugna pacos -Vicugna vicugna -Vigna -Vigna aconitifolia -Vigna angularis -Vigna angularis var. nipponensis -Vigna glabrescens -Vigna hainiana -Vigna marina -Vigna mungo -Vigna mungo var. mungo -Vigna radiata -Vigna radiata var. radiata -Vigna radiata var. sublobata -Vigna riukiuensis -Vigna silvestris -Vigna stipulacea -Vigna subterranea -Vigna trilobata -Vigna umbellata -Vigna unguiculata -Vigna unguiculata subsp. sesquipedalis -Vigna unguiculata subsp. unguiculata -Vigna vexillata -Villa sp. -Vinca -Vinca major -Vinca minor -Vincetoxicum acuminatum -Vincetoxicum indicum -Viola arvensis -Viola canadensis -Viola grypoceras -Viola odorata -Viola philippica -Viola prionantha -Viola tricolor -Viola verecunda -Viola x wittrockiana -Vipera aspis aspis -Vipera transcaucasiana -Vireo griseus -Vireo olivaceus -Virgibacillus halotolerans -Viridiplantae -Vitis -Vitis aestivalis -Vitis amurensis -Vitis berlandieri -Vitis californica -Vitis cinerea -Vitis cinerea var. helleri x Vitis riparia -Vitis coignetiae -Vitis flexuosa -Vitis hybrid cultivar -Vitis hybrid rootstock -Vitis labrusca -Vitis labrusca x Vitis vinifera -Vitis monticola -Vitis quinquangularis -Vitis riparia -Vitis rotundifolia -Vitis rupestris -Vitis shuttleworthii -Vitis sp. -Vitis vinifera -Vitis vinifera x Vitis labrusca -Vitis vulpina -Vitis x champinii -Vitis x labruscana -Vitis x labruscana x Vitis vinifera -Vitrella brassicaformis -Vittaria lineata -Viverricula indica -Viverridae -Vochysia rufa -Volemys millicens -Volkameria inermis -Volucella zonaria -Volvox aureus -Vombatus ursinus -Vulpes -Vulpes chama -Vulpes corsac -Vulpes lagopus -Vulpes macrotis -Vulpes vulpes -Vulpes zerda -Vultur gryphus -Wahlenbergia marginata -Waitea circinata -Walkerella -Walkerella benjamini -Wallemia sebi -Wasmannia auropunctata -Watasenia scintillans -Weigela florida -Weissella ceti -Weissella cibaria -Weissella confusa -Weissella sp. -Welwitschia mirabilis -Whitmania pigra -Willdenowia -Willisornis poecilinotus -Winogradskyella -Wiseana cervinata -Wissadula -Wissadula amplissima -Wisteria -Wisteria brachybotrys -Wisteria floribunda -Wisteria sinensis -Withania somnifera -Wolbachia -Wolbachia endosymbiont -Wolbachia endosymbiont of Adalia bipunctata -Wolbachia endosymbiont of Apocryptophagus sp. -Wolbachia endosymbiont of Armadillidium vulgare -Wolbachia endosymbiont of Armigeres kesseli -Wolbachia endosymbiont of Asobara japonica -Wolbachia endosymbiont of Asobara rufescens -Wolbachia endosymbiont of Blattella sp. -Wolbachia endosymbiont of Bracon hebetor -Wolbachia endosymbiont of Cadra cautella -Wolbachia endosymbiont of Ceratosolen emarginatus -Wolbachia endosymbiont of Ceratosolen solmsi -Wolbachia endosymbiont of Chorthippus parallelus -Wolbachia endosymbiont of Coleosoma octomaculatum -Wolbachia endosymbiont of Coquillettidia crassipes -Wolbachia endosymbiont of Corcyra cephalonica -Wolbachia endosymbiont of Culex fuscocephala -Wolbachia endosymbiont of Culex gelidus -Wolbachia endosymbiont of Culex quinquefasciatus -Wolbachia endosymbiont of Drosophila melanogaster -Wolbachia endosymbiont of Drosophila simulans -Wolbachia endosymbiont of Encarsia formosa -Wolbachia endosymbiont of Eupristina koningsbergeri -Wolbachia endosymbiont of Folsomia candida -Wolbachia endosymbiont of Hylyphantes graminicola -Wolbachia endosymbiont of Hypolimnas bolina -Wolbachia endosymbiont of Laodelphax striatellus -Wolbachia endosymbiont of Leptopilina clavipes -Wolbachia endosymbiont of Leptopilina guineinsis -Wolbachia endosymbiont of Leptopilina heterotoma -Wolbachia endosymbiont of Lissorhoptrus oryzophilus -Wolbachia endosymbiont of Mansonia indiana -Wolbachia endosymbiont of Mansonia uniformis -Wolbachia endosymbiont of Megalothorax incertus -Wolbachia endosymbiont of Mesaphorura yosii -Wolbachia endosymbiont of Muscidifurax uniraptor -Wolbachia endosymbiont of Neoscona vigilans -Wolbachia endosymbiont of Nephila clavata -Wolbachia endosymbiont of Nilaparvata lugens -Wolbachia endosymbiont of Nurscia albofasciata -Wolbachia endosymbiont of Oxyopes sertatus -Wolbachia endosymbiont of Philotrypesis pilosa -Wolbachia endosymbiont of Philotrypesis sp. 1 -Wolbachia endosymbiont of Pholcus crypticolens -Wolbachia endosymbiont of Prosoponoides sinensis -Wolbachia endosymbiont of Simulium squamosum -Wolbachia endosymbiont of Sogatella furcifera -Wolbachia endosymbiont of Supella longipalpa -Wolbachia endosymbiont of Sycoscapter sp. 1 -Wolbachia endosymbiont of Trichogramma kaykai -Wolbachia endosymbiont of Trichopria drosophilae -Wolbachia endosymbiont of Tripteroides aranoides -Wolbachia endosymbiont of Walkerella benjamini -Wolbachia endosymbiont of Walkerella sp. -Wolbachia endosymbiont wVitB of Nasonia vitripennis -Wolbachia pipientis -Wolbachia sp. -Wolbachia sp. wCauB -Wolbachia sp. wMel_AMD -Wolbachia sp. wMel_KL -Woodsia scopulina -Wyeomyia -Wyeomyia complosa -Wyeomyia melanocephala -x Aranda -x Doritaenopsis -x Sorbaronia -x Triticosecale -Xanthium strumarium -Xanthocnemis zealandica -Xanthocryptus novozealandicus -Xanthogaleruca luteola -Xanthomonas -Xanthomonas albilineans -Xanthomonas arboricola -Xanthomonas arboricola pv. juglandis -Xanthomonas axonopodis -Xanthomonas campestris -Xanthomonas campestris pv. campestris -Xanthomonas campestris pv. campestris str. 8004 -Xanthomonas campestris pv. pelargonii -Xanthomonas citri -Xanthomonas citri subsp. citri Aw12879 -Xanthomonas euvesicatoria -Xanthomonas fragariae -Xanthomonas oryzae -Xanthomonas oryzae ATCC 35933 -Xanthomonas oryzae pv. oryzae -Xanthomonas oryzae pv. oryzicola -Xanthomonas perforans -Xanthomonas sp. -Xanthomonas translucens pv. translucens DSM 18974 -Xanthomonas vesicatoria -Xanthonycticebus pygmaeus -Xanthoria parietina -Xanthosoma -Xanthosoma mafaffa -Xanthosoma riedelianum -Xanthosoma sagittifolium -Xenophyes metoponcus -Xenophysella greensladeae -Xenopus laevis -Xenosaurus platyceps -Xenotilapia -Xenotilapia boulengeri -Xenotilapia nasus -Xenotilapia sp. 'spilopterus north' AB-2019 -Xerochrysum bracteatum -Xipholeptos notoides -Xiphophorus birchmanni -Xiphophorus hellerii -Xiphophorus maculatus -Xiphophorus malinche x Xiphophorus birchmanni -Xylella -Xylella fastidiosa -Xylocopa iris -Xylocopa sp. -Xylocopa valga -Xylocopa violacea -Xylocopa virginica -Xylophilus sp. -Xysticus cristatus -Yersinia -Yersinia enterocolitica -Yersinia enterocolitica (type O:3) -Yersinia pestis -Yersinia pestis A1122 -Yersinia pestis EV76-CN -Yersinia pseudotuberculosis -Yersinia ruckeri -Yersinia sp. (in: enterobacteria) -Yucca aloifolia -Yucca gloriosa -Zalophus californianus -Zalophus californianus californianus -Zamenis situla -Zamioculcas zamiifolia -Zantedeschia -Zantedeschia aethiopica -Zantedeschia jucunda -Zanthoxylum -Zanthoxylum armatum -Zea diploperennis -Zea mays -Zea mays subsp. mays -Zenaida -Zenaida macroura -Zephyranthes candida -Zeugodacus cucurbitae -Zeugodacus tau -Zeus faber -Zicrona caerulea -Zingiber mioga -Zingiber officinale -Zingiber striolatum -Zinnia -Zinnia bicolor -Zinnia elegans -Ziphius cavirostris -Zizania latifolia -Ziziphus jujuba -Ziziphus lotus -Ziziphus montana -Zoarces viviparus -Zonotrichia -Zonotrichia albicollis -Zonotrichia capensis -Zonotrichia leucophrys -Zoothera dauma -Zootoca vivipara -Zophobas atratus -Zophobas morio -Zostera marina -Zostera muelleri -Zosteropidae -Zosterops erythropleurus -Zosterops japonicus -Zosterops lateralis -Zoysia matrella -Zygodontomys brevicauda -Zygodontomys cherriei -Zygosaccharomyces bailii -Zymoseptoria tritici diff --git a/Code/Code_Dev/host.jl b/Code/Code_Dev/host.jl index b74b091..45445f5 100644 --- a/Code/Code_Dev/host.jl +++ b/Code/Code_Dev/host.jl @@ -1,5 +1,5 @@ -using NCBITaxonomy using DataFrames +using NCBITaxonomy import CSV include(joinpath(pwd(), "Code/Code_Dev/taxonomizer.jl")) diff --git a/Code/Code_Dev/pathogen.jl b/Code/Code_Dev/pathogen.jl index be621fe..68c004c 100644 --- a/Code/Code_Dev/pathogen.jl +++ b/Code/Code_Dev/pathogen.jl @@ -1,5 +1,5 @@ -using NCBITaxonomy using DataFrames +using NCBITaxonomy import CSV using ProgressMeter diff --git a/Code/Code_Dev/virus.jl b/Code/Code_Dev/virus.jl index de23ca7..e6a7b7e 100644 --- a/Code/Code_Dev/virus.jl +++ b/Code/Code_Dev/virus.jl @@ -1,5 +1,5 @@ -using NCBITaxonomy using DataFrames +using NCBITaxonomy import CSV include(joinpath(pwd(), "Code/Code_Dev/taxonomizer.jl")) diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..e69de29 diff --git a/Intermediate/Formatted/GenbankFormatted.csv.gz b/Intermediate/Formatted/GenbankFormatted.csv.gz index 4731e62..3fbbcec 100644 Binary files a/Intermediate/Formatted/GenbankFormatted.csv.gz and b/Intermediate/Formatted/GenbankFormatted.csv.gz differ diff --git a/Intermediate/Unformatted/GenBankUnformatted.csv.gz b/Intermediate/Unformatted/GenBankUnformatted.csv.gz index 963848a..4fdec8a 100644 Binary files a/Intermediate/Unformatted/GenBankUnformatted.csv.gz and b/Intermediate/Unformatted/GenBankUnformatted.csv.gz differ