Repositories list

• RDPTools

  Public
  Collection of commonly used RDP Tools for easy building

  bioinformaticsmicrobiologymicrobiome+ 3bayesian-classifiers16ssequence-alignment

  Makefile

  •52•49•23•0•Updated Jun 8, 2023Jun 8, 2023

• classifier

  Public
  RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

  Java

  •

  GNU General Public License v2.0

  •32•56•22•1•Updated Dec 21, 2022Dec 21, 2022

• gfclassify

  Public
  Gene Family Classifier allows for fast and accurate classification of amplicon (or open reading frame) nucleotide sequences.

  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jul 29, 2022Jul 29, 2022

• Xander-HMMgs

  Public
  Java

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Dec 29, 2020Dec 29, 2020

• TaxonomyTree

  Public
  TaxonomyTree building and traversal utility classes.

  Java

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Dec 29, 2020Dec 29, 2020

• SequenceMatch

  Public
  K-mer based sequence matching tool

  Java

  •

  GNU General Public License v3.0

  •2•1•0•1•Updated Dec 29, 2020Dec 29, 2020

• SeqFilters

  Public
  Java filtering framework for sequence data

  Java

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Dec 29, 2020Dec 29, 2020

• ReadSeq

  Public
  Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package.

  Java

  •

  GNU General Public License v3.0

  •6•1•1•0•Updated Dec 29, 2020Dec 29, 2020

• ProbeMatch

  Public
  Tools for finding (and removing) DNA/RNA primers in sequence reads.

  Java

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated Dec 29, 2020Dec 29, 2020

• KmerFilter

  Public
  Tools for kmer analysis.

  Java

  •

  GNU General Public License v3.0

  •1•0•1•0•Updated Dec 29, 2020Dec 29, 2020

• Framebot

  Public
  Dynamic programming based frame shift detection and correction tool with nearest neighbor classification.

  Java

  •

  GNU General Public License v3.0

  •7•7•3•0•Updated Dec 29, 2020Dec 29, 2020

• AlignmentTools

  Public
  Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package.

  Java

  •

  GNU General Public License v3.0

  •4•1•1•0•Updated Dec 29, 2020Dec 29, 2020

• AbundanceStats

  Public
  Java code for various ecological abundance statistics

  Java

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 29, 2020Dec 29, 2020

• EcoFunPrimer

  Public
  primer design pipeline

  environmentbioinformaticsprimer-design+ 2nucleotide-sequencesprimerdesign

  Java

  •

  GNU General Public License v3.0

  •4•7•5•0•Updated Apr 9, 2020Apr 9, 2020

• Clustering

  Public
  RDP memory-constrained hierarchical clustering tools.

  Java

  •

  GNU General Public License v3.0

  •4•1•0•0•Updated Apr 8, 2020Apr 8, 2020

• Xander_assembler

  Public
  A gene-targeted assembler tool

  Shell

  •4•19•5•1•Updated Oct 27, 2017Oct 27, 2017

• fungene_pipeline

  Public
  Scripts and resources for analyzing sequence data for select eco-functional genes

  Python

  •11•19•3•1•Updated May 25, 2017May 25, 2017

• kb_rdptools

  Public
  kbase app for rdp classifier

  0•0•0•0•Updated Feb 9, 2017Feb 9, 2017

• FungeneUtils

  Public
  FungeneUtils package

  Java

  •1•0•0•0•Updated Jan 10, 2014Jan 10, 2014

• SOAP-examples

  Public
  Code samples from various languages for interacting with RDP soap services

  Perl

  •

  Other

  •0•0•0•0•Updated Oct 24, 2012Oct 24, 2012