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Updated: Sep 28, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
SHOOT: phylogenetic gene search and ortholog inference
David Mark Emms1, Steven Kelly2
1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK. davidmemms@gmail.com.
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 .
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