SHOOT: phylogenetic gene search and ortholog inference

Genome Biol. 2022 Mar 28;23(1):85. doi: 10.1186/s13059-022-02652-8.


Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional tree inference, and it can identify orthologs with high accuracy. In summary, SHOOT is a fast and accurate tool for phylogenetic analyses of novel query sequences. It is available online at .

Keywords: Orthology inference; Phylogenetic tree inference; Sequence similarity search.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Biological Evolution*
  • Phylogeny