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

1# download repo from metagenlab
2git clone https://github.com/metagenlab/eutils.git
3
4# move to eutils directory
5cd eutils
6# add path to pythonpath and path
7echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc
8echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc
9source ~/.bashrc

• 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