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

1. clone eutils repository

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

2. install miniconda
3. 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

The list of available genome assemblies can be downloaded with the script get_genomes_chlassification.py

1df -h

Download gbff files

1df -h