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 its expecting 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 their 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 your analysis of your trees. Please use --help to see all the flags available!

tip

This tool utilizes multiple cores by default so when running this analysis please request more than one CPU core to speed things up!

Parallel Capabilities: Multithreaded by default.