SHOOT.bio - the phylogenetic search engine

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

Using the SHOOT command line tool

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.

Preparing a SHOOT phylogenetic database

0. 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
1. 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/
2. Run python create_shoot_db.py RESULTS_DIRECTORY full, replacing "RESULTS_DIRECTORY" with the path to the OrthoFinder results directory from step 1.
3. Resolve polytomies (only necessary if using EPA-ng): python bifurcating_trees.py RESULTS_DIRECTORY

The OrthoFinder RESULTS_DIRECTORY is now a SHOOT database.

Running SHOOT

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.