Software for Computational Analysis of gene Family Evolution

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 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.

The necessary inputs for CAFE v4.2 are:

1. a data file containing gene family sizes for the taxa included in the phylogenetic tree
2. a Newick formatted phylogenetic tree, including branch lengths

From the inputs above, CAFE v4.2 will compute:

1. the maximum likelihood value of the birth & death parameter, λ (or of separate birth and death parameters (λ and μ, respectively), over the whole tree or for user-specified subsets of branches in the tree
2. ancestral states of gene family sizes for each node in the phylogenetic tree
3. p-values for each gene family describing the likelihood of the observed sizes given average rates of gain and loss
4. average gene family expansion along each branch in the tree
5. numbers of gene families with expansions, contractions, or no change along each branch in the tree

Run "configure" and "make" from the home directory. The only result is the "cafe" executable in the release directory. This file should be copied to a convenient location.

CAFE v3.0 was a major update to CAFE v2.1. Major updates in 3.0 included: 1) the ability to correct for genome assembly and annotation error when analyzing gene family evolution using the errormodel command. 2) The ability to estimate separate birth (λ) and death (μ) rates using the lambdamu command. 3) The ability to estimate error in an input data set with iterative use of the errormodel command using the accompanying python script caferror.py. This version also included the addition of the rootdist command to give the user more control over simulations.

CAFE v4.0 was the first release in a regular series of releases in order to make CAFE easier and more user-friendly, in addition to adding features and fixing bugs.