Difference between revisions of "Build a core-genome phylogeny"
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# install [https://conda.io/miniconda.html miniconda] | # install [https://conda.io/miniconda.html miniconda] | ||
# create a dedicated environment and install orthofinder | # create a dedicated environment and install orthofinder | ||
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Revision as of 12:15, 24 October 2018
Overview
This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria.
Setup
- 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
- 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