REvolutionH-tl: Reconstruction of Evolutionary Histories tool
Project description
Bioinformatics tool the reconstruction of evolutionaty histories. Input: best-match data, Output: event labeled gene trees and reconciliations.
- José Antonio Ramírez-Rafael [jose.ramirezra@cinvestav.mx]
- Maribel Hernandez-Rosales [maribel.hr@cinvestav.mx ]
Bioinformatics & complex networks lab
REvolutionHtl analyzes putative best matches for the inference of event-labeled gene trees. Moreover, the tool performs tree reconciliation if a species tree is provided.
If you don't have best-match data, you can use proteinortho and the revolutionhtl.parse_prt module.
Install
pip install --upgrade revolutionhtl
Dependencies
- pandas
- networkx
- os
- itertools
- argparse
- numpy
- tqdm
Usage
The pipeline is divided into 5 modules:
- From proteinortho to putative best matches: revolutionhtl.parse_prt
- From best match graph to event-labeled gene tree: revolutionhtl.is_cBMG
- Convert drigraph to BMG:
- Reconciliation of gene and species trees:
- Visualization:
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