CAFE

CAFE is designed to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. It utilizes a birth and death process to model gene gain and loss across a specified phylogenetic tree.

For input, CAFE expects a Newick-formatted phylogenetic tree that includes branch lengths, as well as a tab delimited gene families file to be analyzed.

For more information, please see the CAFE GitHub page.

To load CAFE on Palmetto 2, run the following:

module load biocontainers
module load cafe

To run an analysis with CAFE, the command would look roughly like:

cafe5 --infile INPUT --tree TREEFILE

tip

This tool has several flags to help refine the analysis of your trees. Please use --help to see all the flags available!

tip

This tool utilizes multiple cores by default, so you may request more than one CPU core to speed things up when running a CAFE analysis!

Parallel Capabilities: Multithreaded by default.