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: 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 ]
Install
pip install revolutionhtl
Requirements
If you want to run sequence alignments using revolutionhtl, then install Diamond.
Usage
python -m revolutionhtl <arguments>
Pipeline
- 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).
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