Difference between revisions of "Build a core-genome phylogeny"
Jump to navigation
Jump to search
(Created page with " == Overview == This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria. === Setup === * clone the necessary rep...") |
|||
| Line 9: | Line 9: | ||
* clone the necessary repositories | * clone the necessary repositories | ||
| + | |||
| + | * install miniconda | ||
| + | * create a dedicated environment and install orthofinder | ||
| + | |||
| + | <syntaxhighlight lang="Bash" line='line'> | ||
| + | conda create -n orthofinder | ||
| + | source activate orthofinder | ||
| + | conda install orthofinder | ||
| + | </syntaxhighlight> | ||
Revision as of 10:53, 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
- 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