SHOOT is a phylogenetic alternative to BLAST. Instead of returning a list of similar sequences to a query sequence it returns a maximum likelihood phylogenetic tree with your query sequence embedded in it.
Try it out: https://shoot.bio/
Preprint: https://www.biorxiv.org/content/10.1101/2021.09.01.458564
SHOOT allows you to search a protein sequence against a database of gene trees. It returns your gene grafted into the correct position within its corresponding gene tree.
- Install dependencies:
- Python libraries: ete3, sklearn, biopython
- DIAMOND
- MAFFT
- EPA-ng & gappa (https://github.com/lczech/gappa)
- Alternatively, IQ-TREE can be used instead of the combination EPA-ng + gappa
- Run an OrthoFinder analysis on your chosen species, using the multiple sequence alginment option for tree inference, "-M msa".
- Paper: Emms, D.M., Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20, 238 (2019). https://doi.org/10.1186/s13059-019-1832-y
- GitHub: https://github.com/davidemms/OrthoFinder
- Tutorials: https://davidemms.github.io/
- Run
python create_shoot_db.py RESULTS_DIRECTORY full, replacing "RESULTS_DIRECTORY" with the path to the OrthoFinder results directory from step 1. - Resolve polytomies (only necessary if using EPA-ng):
python bifurcating_trees.py RESULTS_DIRECTORY
The OrthoFinder RESULTS_DIRECTORY is now a SHOOT database.
python shoot INPUT_FASTA SHOOT_DB
where INPUT_FASTA is a fasta file containing the amino acid sequence for the search and SHOOT_DB is the SHOOT database directory created using the steps above.