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)