Running ParGenes

The ParGenes script is located here. Please make sure that you compiled the source beforehand (with the install script at the root directory).

ParGenes needs an input directory containing MSAs files, and some additional parameters. The script will treat each MSA file simultaneously and independently.

Main features:

For each MSA in a directory:

• Finding the best-fit model with model-test-ng
• ML tree search with raxml-ng, from one or more starting trees, and keep the best one
• Bootstraps trees and branch support values computation