CAFE

Computational Analysis of gene Family Evolution (CAFE)

The current build is based on the bioconda distribution of the Hahn Lab CAFE v.4.2.1.

The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.

CAFE v4.2.1 is the latest in a regular series of releases to the CAFE application. The manual and various tutorials may be viewed on the website (https://hahnlab.github.io/CAFE/) . This document describes how to download and use CAFE v4.2.1. (credits: https://github.com/hahnlab/CAFE)