revolutionhtl 1.0.10

REvolutionH-tl: Reconstruction of Evolutionary Histories tool

Bioinformatics tool for the reconstruction of evolutionary histories. Input: fasta files or sequence alignment hits, Output: orthology. event-labeled gene trees, and reconciliations.

Bioinformatics & complex networks lab

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

Steps

1. Orthogroup & best hit selection. Input: alignment hits (generate this using revolutionhtl.diamond) .
2. Orthology and gene tree reconstruction. Input: best hits (generate this at step 1).
3. Species tree reconstruction. Input: gene trees (generate this at step 2).
4. Tree reconciliation. Input: gene and species trees (generate this at steps 2 and 3).

Install

pip install revolutionhtl

Requirements

Python >=3.7

If you want to run sequence alignments using revolutionhtl, then install Diamond.

Usage

Go to the wiki for details and an example.

python -m revolutionhtl <arguments>

The arguments specify steps to run and parameters.

Specify steps and input data (Click to expand)

- -h --help show this help message and exit

-steps [int ...] List of steps to run (default: 1 2 3 4).

-alignment_h str --alignment_hits str Directory containing alignment hits, the input of step 1. (default: ./).

-best_h str --best_hits str .tsv file containing best hits, the input of step 2. (default: use output of step 1).

-T str --gene_trees str .tsv file containing gene trees, the input of steps 3 and 4. (default: use output of step 2).

-S str --species_tree str .nhx file containing a species tree, an input of step 4. (default: use output of step 3).