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SHOOT: phylogenetic gene search and ortholog inference

View ORCID ProfileD.M. Emms, View ORCID ProfileS. Kelly
doi: https://doi.org/10.1101/2021.09.01.458564
D.M. Emms
1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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  • For correspondence: david.emms@plants.ox.ac.uk steven.kelly@plants.ox.ac.uk
S. Kelly
1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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  • For correspondence: david.emms@plants.ox.ac.uk steven.kelly@plants.ox.ac.uk
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Abstract

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://shoot.bio/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 03, 2021.
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SHOOT: phylogenetic gene search and ortholog inference
D.M. Emms, S. Kelly
bioRxiv 2021.09.01.458564; doi: https://doi.org/10.1101/2021.09.01.458564
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SHOOT: phylogenetic gene search and ortholog inference
D.M. Emms, S. Kelly
bioRxiv 2021.09.01.458564; doi: https://doi.org/10.1101/2021.09.01.458564

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