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
   

1. install miniconda
2. 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