Build a core-genome phylogeny

Overview

This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria.

Setup

• clone the necessary repositories

• install miniconda
• create a dedicated environment and install orthofinder

1conda create -n orthofinder
2source activate orthofinder
3conda install orthofinder

Get table of genome assemblies

1df -h

Download gbff files

1df -h