REvolutionH-tl: Reconstruction of Evolutionary Histories tool
Project description
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 [jose.ramirezra@cinvestav.mx]
- Maribel Hernandez-Rosales [maribel.hr@cinvestav.mx ]
Steps
- Orthogroup & best hit selection. Input: alignment hits (generate this using
revolutionhtl.diamond
) . - Orthology and gene tree reconstruction. Input: best hits (generate this at step 1).
- Species tree reconstruction. Input: gene trees (generate this at step 2).
- Tree reconciliation. Input: gene and species trees (generate this at steps 2 and 3).
Install
pip install revolutionhtl
Requirements
If you want to run sequence alignments using revolutionhtl, then install Diamond.
Usage
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).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
revolutionhtl-1.0.6.tar.gz
(35.5 kB
view hashes)
Built Distribution
Close
Hashes for revolutionhtl-1.0.6-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 69d16b24d7e9b3d79d11a9c83e5c2ad08461dc1f4f32c12ec269dc848bb5c4b0 |
|
MD5 | d433d4e47466557c2bb07e03cbbc1339 |
|
BLAKE2b-256 | d8161f491a56a194ebdf9facfa3aec7add2a87ac47197c69e7e0282f24b7d42f |