Skip to content

Produce phylogenomic trees with thousands of orthologous gene sequences from OrthoDB. Then only required input is a species list (species must be present in OrthoDB).

Notifications You must be signed in to change notification settings

laruzzante/orthophile

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

59 Commits
 
 
 
 
 
 
 
 

Repository files navigation

Orthophile

Snakemake pipeline to build phylogenetic trees with thousand of orthologues genes from OrthoDB.

Usage

Install conda or miniconda (https://docs.conda.io/projects/conda/en/latest/user-guide/install/).

Download the orthophile git repository.

Open a terminal and move into the orthophile folder: cd <your/path/to/orthophile>

Move into the workflow folder: cd workflow

Prepare an input file containing the list of species that you would like to include in the phylogeny, using this format (one species per row): NCBI_taxonomy_ID, species_name where 'species_name' can be any name you want to associate to that species, followed by a comma and its corresponding NCBI Taxonomy identifier. Any white spaces in the species names should be replaced by underscores ('_').

Edit the configuration file config.yaml (specify your orthologous group selection parameters and RAxML parameters).

Rune the pipeline, where N is the number of cores you want snakemake to use: snakemake --cores <N> --use-conda

The RAxML results will be stored in a specific folder in the output.

About

Produce phylogenomic trees with thousands of orthologous gene sequences from OrthoDB. Then only required input is a species list (species must be present in OrthoDB).

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages