Difference between revisions of "Build a core-genome phylogeny"
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* clone the necessary repositories | * clone the necessary repositories | ||
| + | |||
| + | <syntaxhighlight lang="Bash" line='line'> | ||
| + | git clone https://github.com/metagenlab/eutils.git | ||
| + | </syntaxhighlight> | ||
* install miniconda | * install miniconda | ||
Revision as of 10:56, 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
1conda create -n orthofinder
2source activate orthofinder
3conda install orthofinder
Get table of genome assemblies
1df -h
Download gbff files
1df -h