Michael Byars ([email protected]) Simone Gable ([email protected]) Tollis Lab

Based off of: https://bioinformaticsworkbook.org/dataAnalysis/phylogenetics/reconstructing-species-phylogenetic-tree-with-busco-genes-using-maximum-liklihood-method.html#gsc.tab=0

Software Dependencies

BUSCO (version 3.0, not compatible with version 4.0+) MAFFT: https://mafft.cbrc.jp/alignment/software/ RAxML-HPC: https://cme.h-its.org/exelixis/web/software/raxml/index.html TrimAL: https://github.com/scapella/trimal ASTRAL: https://github.com/smirarab/ASTRAL

Installation Instructions

1.) Clone github repository

2.) Create Conda environments using the bioconda recipes for the following programs

MAFFT: https://mafft.cbrc.jp/alignment/software/ RAxML-HPC: https://cme.h-its.org/exelixis/web/software/raxml/index.html TrimAL: https://github.com/scapella/trimal

3.) Export .yaml files for each environment into the folder /YOUR_WORKING_DIR/busco_phylo_pipeline/conda_yamls

4.) Conda .yaml files should have the following names to work with snakake pipeline:

amas.yml mafft.yml raxml.yml trimal.yml

5.) Download and install astral into the tools/ directory

Note: If you are using a different version of Astral you will have to correct the name in the Snakemake pipeline

6.) Extract nucleotide sequences for each BUSCO, place in the data/busco_nt_merged/ directory

Helper Scripts have been placed in the scripts/ directory to help automate this process. Run busco_multiseq_generator.sh in the base directory of your BUSCO output directory to extract and collate the sequences into one file containing the sequences from every species for each BUSCO. If you have transcriptome mode output from BUSCO there is a script called trans_extract_sequences.sh that you will need to run on each transcriptome mode run before running busco_multiseq_generator.sh.

Run the Snakemake Pipeline use this command (or similar)

snakemake --cores 4 --use-conda --keep-going