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