revolutionhtl 1.0.11

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>

See bellow the full list of arguments

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).

File names (Click to expand)

-o str --output_prefix str
Prefix used for output files (default "tl_project"). -og str --orthogroup_column str
Column in -best_h -T, and output files specifying orthogroups (default: OG). -Nm int --N_max int
Indicates the maximum number of genes in a orthogroup, bigger orthogroups are splitted. If 0, no orthogroup is splitted. (default= 2000). -k int --k_size_partition int
Integer indicatng how many best hit graphs will be processed in bunch:: first graphs with