Difference between revisions of "Build a core-genome phylogeny"
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<syntaxhighlight lang="Bash" line='line'> | <syntaxhighlight lang="Bash" line='line'> | ||
| + | # create a new environment | ||
conda create -n orthofinder | conda create -n orthofinder | ||
source activate orthofinder | source activate orthofinder | ||
| + | # install orthofinder | ||
conda install orthofinder | conda install orthofinder | ||
| + | # install biopython | ||
| + | conda install biopython | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 12:01, 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 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