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REvolutionH-tl: Reconstruction of Evolutionary Histories tool

Project description

REvolutionH-tl logo.

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

Install

pip install revolutionh-tl

Requirements

For sequence alignments using revolutionhtl: Diamond

Usage

Go to the wiki for details and an example.

python -m revolutionhtl <arguments>

Pipeline

  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).

pipeline{width=80%}

Project details


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