FUSE-PhyloTree enables to identify sequence conservation modules and associate them with functional annotations through phylogenomic analysis.
Introducing an original approach to characterizing functional motifs. This methodology encompasses:
- Detection of conserved sequence modules (using Partial Local Multiple Alignment)
- Phylogenetic inference of species/genes/modules/functions evolutionary histories
- Identification of co-appearances of modules and functions
The process considers protein sequences and their associated functional annotations as input. It then returns the presence of the conserved sequence modules and of the functional annotations in each ancestral gene along the gene phylogeny.
Detailed Pipeline
Detailed flowchart of the pipeline:
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U@{ shape: manual-input, label: "User Input"} --> A
U --> B
U --> C
A@{ shape: doc, label: "sequences.fasta" } --> m1@{ shape: rectangle, label: "modules_segm.py: segmentation_and_module_phylo()"}
m1 --> m2@{ shape: docs, label: "module_segm_dir_seq/" }
m2 --> m3@{ shape: rectangle, label: "tools.py: segmentation()"}
m5@{ shape: flag, label: "paloma-D" } o--o|call| m3
m3 --> m4@{ shape: doc, label: "seq_filename.dot" }
m4 --> m6@{ shape: rectangle, label: "tools.py: modules_fasta()"}
m6 --> m7@{ shape: docs, label: "module_seq/*.fasta" }
m7 --> m8@{ shape: rectangle, label: "tools.py: all_phylo()"}
m9@{ shape: flag, label: "PhyML" } o--o|call| m8
m8 --> m12@{ shape: docs, label: "module_seq/*.tree" }
m12 --> m10@{ shape: rectangle, label: "modules_segm.py: correct_modules_tree()"}
m11@{ shape: flag, label: "TreeFix" } o--o|call| m10
m10 --> m13@{ shape: docs, label: "module_seq/*.treefix.tree" }
m10 --> m14@{ shape: doc, label: "modules_path_modules.txt" }
m13 o--o|describe paths of| m14
B@{ shape: doc, label: "sequences.tree" } --> g1{gene tree as input ?}
g1 -->|yes| g2@{ shape: doc, label: "rooted binary gene tree .tree" }
g1 -->|no| g3@{ shape: rectangle, label: "gene_phylo.py: whole_phylo()"}
A -.-> g3
g4@{ shape: flag, label: "Muscle" } o--o|call| g3
g5@{ shape: flag, label: "TrimAl" } o--o|call| g3
g6@{ shape: flag, label: "PhyML" } o--o|call| g3
g7@{ shape: flag, label: "TreeFix" } o--o|call| g3
g8@{ shape: flag, label: "PhyML (branch len)" } o--o|call| g3
g3 --> g2
A --> s1@{ shape: rectangle, label: "species_phylo.py: taxid_from_fasta()"}
s2@{ shape: cyl, label: "NCBI Taxonomy" } o--o|use| s1
s1 --> s3@{ shape: doc, label: "species.tree" }
A --> d1@{ shape: rectangle, label: "tools.py: known_domains()"}
d1 --> d2@{ shape: doc, label: "domains.csv" }
g2 --> r1@{ shape: rectangle, label: "tools.py: seadog_md()"}
m14 --> r1
s3 --> r1
r2@{ shape: flag, label: "Seadog-MD" } o--o|call| r1
r1 --> r3@{ shape: doc, label: "seadogMD.output" }
r3 --> r4@{ shape: rectangle, label: "integrates_3phylo.py: write_sp_gene_event()"}
r4 --> r5@{ shape: doc, label: "seadogMD_sp_gene_event.csv" }
r4 --> r6@{ shape: doc, label: "seadogMD_gene.tree" }
C@{ shape: doc, label: "functional annotations.csv" } --> a1@{ shape: rectangle, label: "ances_scenario.py: acs_inference()"}
r5 --> a1
r6 --> a1
a1 --> a2@{ shape: doc, label: "pastml_seadogMD.csv" }
a2 --> a3@{ shape: rectangle, label: "tools.py: pastml()"}
a4@{ shape: flag, label: "PastML" } o--o|call| a3
a3 --> a5@{ shape: doc, label: "pastml_seadogMD_combined_ancestral_states.tab" }
a3 --> a6@{ shape: docs, label: "acs_dir_seadogMD/" }
r3 --> i1@{ shape: rectangle, label: "integrate_3phylo.py: __main__()"}
g2 --> i1
a5 --> i1
d2 --> i1
i1 --> i2@{ shape: doc, label: "0_gene.tree" }
i1 --> i3@{ shape: doc, label: "1_modules_and_functions_evolution.csv" }
i1 --> i4@{ shape: doc, label: "2_module_descriptions.csv" }
i1 --> i5@{ shape: docs, label: "3_visuReconc/" }
i1 --> i6@{ shape: docs, label: "working_dir/" }
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Legend of the detailed pipeline
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❓ Differences from PhyloCharMod: FUSE-PhyloTree is an actively maintained fork of PhyloCharMod, originally developed for studying the ADAMTS-TSL protein family.
Application note in preparation
For a more detailed explanation of the methodology, refer to the following article [Dennler et al. 2023], or the following PhD thesis (only available in French).
To run the full pipeline, simply use:
python3 fuse-phylotree.py <sequences.fasta> <annotations.csv> <gene_tree.tree>
To install and run this command, you need a proper environment. We strongly recommend using the available Docker image (recommended for personal computers) or Singularity image (recommended for high-performance computing clusters).
-
<sequences.fasta>:Each sequence header must satisfies the format:
>SeqID_taxid, whereSeqIDrepresents the unique sequence identifier andtaxidis the NCBI species taxid (e.g.,>NP031426.2_10090)>NP00001.1_9913 MKAAPTKARREGALVV >XP00002.1_9606 MKVAPTTKAKRGVLVA >NP00003.1_7955 MTKARRMTGGIW >NP00004.3_9606 MTKARRMTGGLLAVRefer to this file for an example
Please refrain from using special characters in the header (e.g.
, |,()`":;). Use only_as a separator.These files can be generated using orthogroups and GFF files, all of which are included in the Docker and Singularity images for nine species (Homo sapiens, Mus musculus, Bos taurus, Gallus gallus, Xenopus tropicalis, Danio rerio, Ciona intestinalis, Drosophila melanogaster, Caenorhabditis elegans). You only need to provide a file with a list of RefSeq of interest. For detailed instructions, please refer to To build a sequence dataset based on orthogroups.
-
<annotations.csv>:This file contains the functional annotations associated with the different sequences (e.g., PPI)
Each line should be formatted as:
SeqID,Annotation_1|Annotation_2. Here,SeqIDis the unique sequence identifier. It is separated from the list of annotations by a comma (,), and individual annotations are separated by pipe symbols (|) (e.g.,NP_620594.1,P00451_F8|P04275_VWF). Annotations must have more than one character in length.NP_00001.1,Interact_with_A|Interact_with_B XP_00002.1,Interact_with_A|Interact_with_B NP_00003.1,Interact_with_A NP_00004.3,Interact_with_ARefer to this file for an example
-
<gene_tree.tree>:This file contains a binary rooted gene tree of the sequences in newick format.
((NP_00001.1:0.16,XP_00002.1:0.23):0.87,(NP_00003.1:0.35,NP_00004.3:0.42):0.47);Refer to this file for an example
💡 For other option
Pre-computed phylogenetic trees or/and paloma module decompositions can be use, as long as they respect the required header format.
usage: fuse-phylotree.py [-h] [--output_directory OUTPUT_DIRECTORY] [--species_tree SPECIES_TREE] [--infer_gene_tree INFER_GENE_TREE] [--plma_file PLMA_FILE] [--reconc_domains] multi_fasta_file leaf_functions_csv [gene_tree]
positional arguments:
multi_fasta_file Multi fasta file, with specific formated header >RefSeq_taxid (ex : >XP_012810820.2_8364)
leaf_functions_csv csv file containing for each of our sequence, the list of his functions (ex : XP_012810820.2, P59509 | P999999)
gene_tree Gene tree to use as a support for the pastML and DGS reconciliation inference (WARNING, must correspond to the sequences in the multi fasta file !)
optional arguments:
-h, --help show this help message and exit
--output_directory OUTPUT_DIRECTORY
output directory name
--species_tree SPECIES_TREE
Species tree to use as a support for the reconciliations (WARNING, must correspond to the taxid use in the other files !)
--infer_gene_tree INFER_GENE_TREE
Infer gene tree to use as a support for the pastML and DGS reconciliation inference (WARNING, user should check it and reroot it - we advise to only use it if you know what you are doing !)
--plma_file PLMA_FILE
Paloma-2 output file (.agraph format, .dot, or .oplma format)
--reconc_domains Do a DGS reconciliation with known modules (pfam / prosite)
⚠️ Infering the gene tree using the pipeline option--infer_gene_treeWhen running the analysis without a gene tree as input (with--infer_gene_tree INFER_GENE_TREE), a default rooted tree will be generated (note that you must explicitly include the keywordINFER_GENE_TREEas the parameter for this option to confirm that you intend to perform this step). However, for optimal results, it is strongly recommended to infer a properly rooted gene tree prior to analysis and use it as the input for the gene_tree option. The gene phylogenetic tree serves as a critical template for the entire analysis, thus it is essential that a reliable and accurately rooted gene tree is prepared and utilized.
The main workflow output is the list of modules and functions that are present, gained or lost at the different ancestral genes. This output is presented as a table in the file 1_modules_and_functions_evolution.csv (Example here). It is strongly advised to also look at the final gene tree (with internal node names) 0_gene.tree to visualise the annotated gene nodes. The file 0_gene.tree corresponds to the input phylogenetic tree and assigns an ancestor name to each internal node. The description of all the modules is available in 2_module_descriptions.csv and it enables to get module segments (sequences and positions) based on module names. For an interactive visualisation of these data, various iTOL files are generated in 3_visuReconc/ and compressed in 3_visuReconc.zip for batch upload on iTOL.
-
0_gene.tree:This file contains the binary rooted gene tree of the sequences in newick format with internal node names.
-
1_modules_and_functions_evolution.csv:This file contains the list of modules and functions that are present, gained or lost at the different ancestral and actual genes, i.e., for all nodes in the gene tree.
-
2_module_descriptions.csv:This file contains all module descriptions: all their segments, proteins, and positions in the protein sequences.
-
3_visuReconc/:This directory contains various iTOL files for the interactive visualisation.
-
Working directory -
working_dir_*:The intermediates outputs obtained at each of the pipeline steps are provided in a directory called
working_dir_*(see this directory for an example)
Detailed Output & Working Directory
working_directory
├── 0_gene.tree -----> file contains the binary rooted gene tree of the sequences in newick format with internal node names
├── 1_modules_and_functions_evolution.csv -----> file contains the list of modules/functions present/gained/lost at the different ancestral and actual genes, i.e., for all nodes in the gene tree
├── 2_module_descriptions.csv -----> file contains all module descriptions: all their segments, proteins, and positions in the protein sequences
├── 3_visuReconc -----> All itol visualisation files
│ ├── geneReconc_seadogMD_*.tree -----> The "final" gene tree after treefix correction / internal node labelling by seadog mDGS reconciliation / branch length computing by PhyML
│ ├── itolAnnotPresence_seadogMD_*.txt -----> Annotation presences in leaves as heatmap
│ ├── itolBarModulesNb_seadogMD_*.txt -----> Module number in leaves as barplot
│ ├── itolDomains_seadogMD_*.txt -----> Domain decompositions as domain mosaics
│ ├── itolGOt_seadogMD_*.txt -----> Annotation presence as symbols
│ ├── itolModPresence_seadogMD_*.txt -----> Module presences in leaves as heatmap
│ ├── itolModTransfer_seadogMD_*.txt -----> Module transfers as arrows
│ ├── itol_modules_PieGainsLost_seadogMD_*.txt -----> Number of modules gained / lost at each gene nodes as a pie charts
│ ├── itolModulesPresent_G*_*_*_only_mod.txt -----> For each gene node * : all module segments in actual gene present at this * (ancestral) gene as domain mosaics (brown squares)
│ ├── itolModules_seadogMD_*.txt -----> Module decompositions as domain mosaics
│ ├── itolModulesThatChanged_G*_*_*_only_mod.txt -----> For each gene node * : all module segments in actual gene gained at this * (ancestral) gene as domain mosaics (green squares)
│ ├── itolPopup_seadogMD_*.txt -----> Gene nodes popup with module and annotation decriptions
│ ├── itol_ppi_PieGainsLost_seadogMD_*.txt -----> Number of modules gained / lost at each gene nodes as a pie charts
│ └── itolSpGeneEvents_seadogMD_*.txt -----> Gene - Species reconcilation events as symbols
├── 3_visuReconc.zip -----> All itol visualisation files compressed for itol batch upload
└── working_dir_*
├── gene.fasta -----> The input fasta file
├── *_species.tree -----> Species tree extracted from ncbi taxonomy
├── leaf_Manual.csv -----> The input with gene functional annotation file
├── gene.tree -----> The input gene tree file (if given as input)
│
├── acs_dir_seadogMD_*_gene -----> All ancestral scenario reconstruction files from pastML
│ ├── leaf_Manual.csv -----> The input with gene functional annotation file
│ ├── pastml_seadogMD_*_gene_leaf_Manual_combined_ancestral_states.tab -----> pastML output regrouping all annotation ancestral states
│ ├── pastml_seadogMD_*_gene_leaf_Manual.csv -----> The input annotation formated as a {0,1,?} matrix for pastML use
│ ├── seadogMD_*_gene_pastml -----> pastML outputs
│ │ ├── marginal_probabilities.character_*.model_*.tab
│ │ ├── params.character_*.method_MPPA.model_*.tab
│ ├── seadogMD_*_gene.tree -----> The "final" gene tree after treefix correction / internal node labelling by seadog mDGS reconciliation / branch length computing by PhyML
│ └── seadogMD_*_sp_gene_event.csv -----> Gene nodes event from Species - Gene reconciliation (e.g., Gene duplication, Speciation)
│
├── gene_phylo_dir_* -----> All tree construction files
│ ├── gene.fasta -----> The input fasta file
│ ├── gene.tree -----> The "final" gene tree after treefix correction / internal node labelling by seadog mDGS reconciliation / branch length computing by PhyML
│ ├── *_species.tree -----> Species tree extracted from ncbi taxonomy
│ ├── muscle_*.fasta -----> Alignment file from muscle
│ ├── phyml_trimal_muscle_*.tree -----> Tree generated by PhyML after alignment with MUSCLE and filtration with trimAl
│ ├── phyml_trimal_muscle_*_treefix_dir -----> Directory containing TreeFix tree correction files
│ │ ├── phyml_trimal_muscle_*.fasta -----> Sequence alignment used for tree correction
│ │ ├── phyml_trimal_muscle_*.tree -----> Initial tree generated by PhyML before correction
│ │ └── phyml_trimal_muscle_*.treefix.tree -----> Tree corrected after treatment with TreeFix
│ ├── phyml_trimal_muscle_*_treefix_dir.smap -----> Node correspondence file between initial tree and corrected tree
│ ├── phyml_trimal_muscle_*_treefix_dir_treeToFixPath.txt -----> Path of the file containing the tree to be corrected
│ ├── trimal_muscle_*.fasta -----> Sequence alignment after filtration with trimAl
│ ├── trimal_muscle_*.phylip -----> Phylip file containing filtered alignment
│ ├── trimal_muscle_*.phylip_phyml_stats.txt -----> Phylogenetic model statistics used by PhyML
│ └── trimal_muscle_*.phylip_phyml_tree.txt -----> Phylogenetic tree generated by PhyML from Phylip alignment
│
├── gene_tree_*
│ └── gene.tree -----> The "final" gene tree after treefix correction / internal node labelling by seadog mDGS reconciliation / branch length computing by PhyML
│
├── modulesChange_seadogMD_*.csv -----> Lists of modules gained / lost at each gene nodes
├── modulesCompo_seadogMD_*.csv -----> Lists of modules presents at each gene nodes
├── modules_paths_modules_*_t*m*M*.txt -----> Define list of module trees to use as seadog input
├── modules_segm_dir_* -----> All modules decomposition files: paloma plma -> for all modules: module fasta -> PhyML tree -> treefix corrected tree
│ ├── *.dnd
│ ├── *.fasta
│ ├── *_t*m*M*.dot -----> The plma file (from input or computed by paloma)
│ ├── *_t*m*M*.oplma
│ ├── *_t*m*M*.plma
│ ├── *_t*m*M*_q*.agraph -----> The plma file (from input or computed by paloma)
│ ├── *_t*M*.afc
│ ├── *.weights
│ └── modules_*_t*m*M*
│ ├── B*.fasta -----> A module fasta file
│ ├── B*.phylip -----> A module in phylip format
│ ├── B*.phylip_phyml_stats.txt -----> PhyML output
│ ├── B*.phylip_phyml_tree.txt -----> PhyML output
│ ├── B*.tree -----> PhyML output
│ ├── B*_treefix_dir -----> treefix working directory
│ │ ├── B*.fasta -----> Module fasta file
│ │ ├── B*.tree -----> Module PhyML tree
│ │ └── B*.treefix.tree -----> Module treefix corrected tree - "final"
│ ├── B*_treefix_dir.smap -----> Gene - Module nodes mapping
│ └── B*_treefix_dir_treeToFixPath.txt -----> Define treefix input
│
├── domains_*.csv -----> Known domains/motifs from scans
├── complete_functionChange_moduleChange_seadogMD_*.csv -----> Table of all annotations and modules gained / lost at each gene nodes (actual and ancestral)
├── functionChange_moduleChange_expand_seadogMD_*.csv -----> Table of modules gained / lost at each gene nodes where there is annotation changes (actual and ancestral) with all module segment details in leaf
├── functionChange_moduleChange_seadogMD_*.csv -----> Table of modules gained / lost at each gene nodes where there is annotation changes (actual and ancestral)
├── seadogMD_*_gene.tree -----> Gene tree from seadog mDGS, with internal gene labelled
├── seadogMD_*.output -----> Seadog mDGS output file
├── seadogMD_*_sp_gene_event.csv -----> Gene nodes event from Species - Gene reconciliation (e.g., Gene duplication, Speciation)
└── specieGeneEvent_seadogMD_*.csv -----> Gene nodes event from Species - Gene reconciliation (e.g., Gene duplication, Speciation)
For ease of use, considering the various software and dependencies required, we strongly recommend using our Docker image. After installing Docker, you can pull our Docker image using the following command:
docker pull ghcr.io/ocmalde/fuse-phylotree:v1.0.0
First, you need to create a container, linked to your workspace, and connect to it interactively:
docker run -it --entrypoint /bin/bash -v "$(pwd):/workspace" -w /workspace ghcr.io/ocmalde/fuse-phylotree:v1.0.0
Then you can simply execute the whole pipeline using:
python3 /fuse-phylotree/fuse-phylotree.py <sequences.fasta> <annotations.csv> <gene_tree.tree>
To quit it, simply type exit
Example with test files provided in the Docker image (you need to connect to the container first):
cd test_dir/ && python3 ../fuse-phylotree/fuse-phylotree.py --infer_gene_tree INFER_GENE_TREE 712buddy37seq.fasta leaf_Manual_712.csv
If you already made a container, you can obtain its <CONTAINER ID> using docker ps -a.
Using the <CONTAINER ID>, you can connect to the existing container with:
docker start <CONTAINER ID> && docker attach <CONTAINER ID>
To use move file from/to the container, use:
docker cp <CONTAINER ID>:/path/in/container/ /path/in/local
On most High Performance Computing clusters, you can directly pull our Singularity image using the following command:
singularity pull fuse-phylotree.sif https://github.com/OcMalde/fuse-phylotree/releases/download/V1.0.0/fuse-phylotree.sif
singularity exec fuse-phylotree.sif python3 /fuse-phylotree/fuse-phylotree.py <sequences.fasta> <annotations.csv> <gene_tree.tree>
Using simple lists of RefSeq IDs proteins and a FUSE-PhyloTree Docker or Singularity image, you can easily generate a formatted FASTA file for the pipeline. This file will contain the longest protein sequence for each homolog (both orthologs and paralogs) in your input family. Simply run one the following script:
Usage: make_orthogroup_fasta.sh <id_seq_file> <name> <docker_image|singularity_image_path>
📑
<id_seq_file>short example:
NP_001987.2
NP_006476.2
NP_006477.2
NP_006478.2
...Refer to this file for the fibulin file example.
Specific modules of the pipeline can be executed independently (see their --help for all usage details).
For example, to compute a phylogenetic tree using Muscle/Trimal/PhyML/Treefix:
python3 /fuse-phylotree/gene_phylo.py <fasta_file> <species_tree>
To only compute the final integration module on computed files:
python3 /fuse-phylotree/integrate_3phylo.py <seadogMD.output> <gene_tree.tree> --pastml_tab <pastml_seadogMD_combined_ancestral_states.tab> --domains_csv <domains.csv>
Example: Running only the final integration step on the fibulin working directory
Move in the working directory (available here):
cd dir_fibuline_phylocharmod
and execute the integration module with:
python3 /fuse-phylotree/integrate_3phylo.py seadogMD_fibulin59.output gene_tree_fibulin59/fibulin59.tree --pastml_tab acs_dir_seadogMD_fibulin59_gene/pastml_seadogMD_fibulin59_gene_leaf_Manual_fibulin59_combined_ancestral_states.tab --domains_csv domains_fibulin59.csv
All the different included softwares are usable using the Docker or Singularity image. For example, paloma-D can be used with:
docker start <CONTAINER ID> && docker exec <CONTAINER ID> /bin/bash -c ". ~/.bashrc && paloma-D --help && exit"
Or simply: paloma-D --help if connected to a container
singularity exec fuse-phylotree.sif paloma-D --help
All these programs are mandatory to run FUSE-PhyloTree, and must be in ;
/usr/local/bin/
If not, their path must be specified in the config file ;
fuse-phylotree/config.txt
Muscle (v3.8.31), one of the best-performing multiple alignment programs, Conda package
PhyML (v3.3.20190909), maximum likelihood phylogenetic inference for the gene and the module trees, Conda package
TreeFix (v1.1.10), Statistically Informed Gene Tree Error Correction Using Species Trees, Conda package
trimAL (v1.4.rev15), Alignment filtering, Conda package
SEADOG-MD, for DGS-reconciliation.
PastML (v1.9.41), for ancestral characters inference, Pip package
paloma-D (v0.1), for sequence segmentation.