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
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