SHOOT: phylogenetic gene search and ortholog inference

David Mark Emms; Steven Kelly

doi:10.1186/s13059-022-02652-8

SHOOT: phylogenetic gene search and ortholog inference

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

Authors

David Mark Emms¹, Steven Kelly²

Affiliations

¹ Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK. davidmemms@gmail.com.
² Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK. steven.kelly@plants.ox.ac.uk.

Abstract

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 www.shoot.bio .

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Biological Evolution*
Phylogeny