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This tutorial

This repository contains a tutorial that should help you get started with CAFE. The tutorial is divided into two parts:

  1. Preparing an input dataset that CAFE understands: this is most of the work, and makes use of auxiliary Python scripts (which we provide) and a few other programs;

  2. Running CAFE: performing basic evolutionary inferences about gene family evolution.

See cafe_tutorial.pdf for details.

Note that this tutorial contains some large data files that are stored in Github LFS format. These files are all intermediate files that can be generated by running the scripts, but if you find it easier or quicker to download the files, you may use the Git LFS client (https://git-lfs.github.com/ ) to do so.