This is a short tutorial on how to get started analyzing FASTA files via the command line.Code is intended for use on an Ubuntu 16.04 LTS OS, but it may work on other Unix or Unix-like systems.Here we will use the ETE3 toolkit, which is a very nice tool for phylogenetic reconstruction. The main website is here: http://etetoolkit.org/We will also look at the EggNOG database, which is a very useful database of protein families: http://eggnogdb.embl.de/#/app/home