Espalier 0.1.2

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests

Espalier

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests. The package can be used to compute maximum agreement forests, compute subtree-prune-and-regraft (SPR) distances, reconcile discordant trees and reconstruct approximate ancestral recombination graphs (ARGs).

For further information on how to use Espalier, please see the primer and documentation pages.

For more information on the algorithms behind Espalier please see:

Rasmussen, D.A. and Guo, F. Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests. 2022.

Installation and set up

The easiest way to install Espalier is through pip:

$ pip install Espalier

pip will install the other Python packages required by Espalier.

However, Espalier also requires but is not packaged with RAxML-NG. Instructions for installing RAxML-NG can be found here.

If Espalier was installed correctly, the command

$ espalier --help

should return the options for Espalier's command line interface.