SHOOT: phylogenetic gene search and ortholog inference
David Emms, Steven Kelly
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 .
Topics & Concepts
Phylogenetic treeBiologyShootTree (set theory)InferenceSequence (biology)Computational biologyGeneEvolutionary biologyGeneticsBotanyComputer scienceArtificial intelligenceMathematicsCombinatoricsGenomics and Phylogenetic StudiesMachine Learning in BioinformaticsGenetic diversity and population structure