revolutionhtl 0.0.5

REvolutionH-tl: Reconstruction of Evolutionary Histories tool

Bioinformatics tool for the reconstruction of evolutionary histories. Input: best-match data, Output: event-labeled gene trees and reconciliations.

Bioinformatics & complex networks lab

• José Antonio Ramírez-Rafael [[e-mail]]
• Maribel Hernandez-Rosales [[e-mail] ]

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REvolutionH-tl analyzes putative best matches for the inference of event-labeled gene trees. Moreover, the tool performs tree reconciliation if a species tree is provided.

If you don't have best-match data, you can use proteinortho and REvolutionH-tl for its generation.

Install

pip install --upgrade revolutionhtl

Dependencies

• pandas
• networkx
• os
• itertools
• argparse
• numpy
• tqdm

Usage

python -m revolutionhtl [-h] [-steps [STEPS ...]] [-prt_path PRT_PATH]
                        [-gene_trees GENE_TREES]
                        [-species_tree SPECIES_TREE] [-hit_list HIT_LIST]
                        [-og ORTHOGROUP_COLUMN] [-o OUTPUT_PREFIX]
                        [-rod RECON_OUTPUT_DIR] [-f F_VALUE]

Arguments

• -h, --help show this help message and exit.
• -steps [STEPS ...] list of steps to run (default: 1 2 3).
• -prt_path PRT_PATH path to a directory containing proteinortho output files.
• -gene_trees GENE_TREES .tsv file containing a .nhx for each line at column "tree"
• -species_tree SPECIES_TREE .nhx file containing a species tree.
• -hit_list HIT_LIST .tsv file containing hits.
• -og ORTHOGROUP_COLUMN, --orthogroup_column ORTHOGROUP_COLUMN column in -hit_list and -gene_trees specifying orthogroups (default: OG).
• -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX prefix used for output files (default "tl_project").
• -rod RECON_OUTPUT_DIR, --recon_output_dir RECON_OUTPUT_DIR directory for reconciliation maps.
• -f F_VALUE, --f_value F_VALUE number between 0 and 1 used for the adaptative threshold for best matches selection (default 0.95, see proteinortho paper for a deep explanation).

Pipeline

The methodology consists of 3 main steps, starting with best-hits data and a species tree. You can use proteinortho and step 0 for the generation of input data.

0. Convert proteinortho output to best-hit list Required arguments: -prt_path Optional arguments: -f
1. Conver best hits to best match graphs (cBMGs) Required arguments: -hit_list
2. Conver cBMGs to gene trees Required arguments: -hit_list
3. Reconciliate gene trees and species tree Required arguments: -gene_trees, -species_tree Optional arguments: -rod

Input data format

-prt_path

A directory containing the output files of proteinortho:

• .proteinortho.tsv file containing orthogroups (*).
• proteinortho_cache/ directory containing bidirectional pairwise BLAST-like analysis (hits).

You can generate these files running proteinortho with the flags -keep, and temp=<the directory used for output files (probably ./)>

(*) An orthogroup is a set of co-orthologous genes.

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-hit_list

A hit is a relationship $x\rightarrow y$, where $x$ is the query accession and $y$ is the target accession. $x$ and $y$ are genes found in different species. Each hit relationship $x\rightarrow y$ is contained in one orthogroup.

The argument -hit_list is a .tsv file containing the columns:

• OG Orthogroup identifier.
• Query_accession Gene identifier.
• Target_accession Gene identifier.
• Query_species Species of the query gene.
• Target_species Species of the target gene.

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-gene_trees

A .tsv file containing the columns:

• OG Orthogroup identifier.
• tree Tree in nhxx format (extended-extended-newick, see here a descripton), where leaf names are gene identifiers, the name of inner nodes are evolutionary events (S for speciation, P for duplication), and leaves have the attribute "species".

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-species_tree

A .nhxx file containing a single species tree in nhxx format (extended-extended-newick, see here a descripton). The name of the leaves must include the species present in the gene tree attributes.

Example

In the directory test_set are three sets of simulated genomes (12noD, 3noD, 5noD).

Let's run the analysis for 12 species:

We will work in the same directory where the data is stored

$ cd 12noD

Use proteinortho for hits and orthogroups assignment.

$ proteinortho6.pl -project=D12 -temp=./ -keep -singles -p=diamond *fa

Create a directory for the storage of reconciliation maps.

$ mkdir recon_maps

Now run revolutionH-tl. Note that we are including step 0, which takes as input the files generate by proteinortho, and outputs a list of best hits.

$ python -m revolutionhtl -steps 0 1 2 3 -species_tree S12.pruned.tree -rod recon_maps

REvolutionH-tl
Running steps 0, 1, 2, 3

Step 0: Convert proteinortho output to a best-hit list
----------------------------------------------------
Reading .proteinortho.tsv file and hits directory...
Selecting best hits by dynamic threshold...
Filtering best hits by orthogroup...
Best hits were successfully written to tl_project.best_hits.tsv
This file will be used as input for step 1.

Step 1: Conver best-hit graphs to cBMGs
---------------------------------------
Reading hit graphs...
Editing to best match graphs (cBMGs)...
Best match graphs successfully written to tl_project.cBMGs.tsv
This file will be used as input for step 2.

Step 2: Reconstruct gene trees
------------------------------
Reading best match graphs...
Reconstructing gene trees...
Labeling gene tree nodes with evolutionary events...
Gene trees were successfully written to tl_project.gene_trees.tsv
This file will be used as input for step 3.

Step 3: Reconciliation of gene species trees
-------------------------------------------
Reading trees...
Reconciling trees...
Resolved gene trees were successfully written to tl_project.resolved_trees.tsv
Reconciliation maps were successfully written at recons/
Indexed species tree successfully written to tl_project.labeled_species_tree.nhxx

In the case when you already have a best-hits list, you can omit step 0, and use the argument -hit_list.

$ python -m revolutionhtl -hit_list tl_project.best_hits.tsv -species_tree S12.pruned.tree -rod recon_maps

REvolutionH-tl
Running steps 1, 2, 3

Step 1: Conver best-hit graphs to cBMGs
---------------------------------------
Reading hit graphs...
Editing to best match graphs (cBMGs)...
Best match graphs successfully written to tl_project.cBMGs.tsv
This file will be used as input for step 2.

Step 2: Reconstruct gene trees
------------------------------
Reading best match graphs...
Reconstructing gene trees...
Labeling gene tree nodes with evolutionary events...
Gene trees were successfully written to tl_project.gene_trees.tsv
This file will be used as input for step 3.

Step 3: Reconciliation of gene species trees
-------------------------------------------
Reading trees...
Reconciling trees...
Resolved gene trees were successfully written to tl_project.resolved_trees.tsv
Reconciliation maps were successfully written at recons/
Indexed species tree successfully written to tl_project.labeled_species_tree.nhxx