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

1git clone https://github.com/metagenlab/eutils.git

• install miniconda
• create a dedicated environment and install orthofinder

1# create a new environment
2conda create -n orthofinder
3source activate orthofinder
4# install orthofinder
5conda install orthofinder
6# install biopython
7conda install biopython

Get table of genome assemblies

1df -h

Download gbff files

1df -h