SHOOT: phylogenetic gene search and ortholog inference

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...

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Detalles Bibliográficos
Autores principales: Emms, David Mark, Kelly, Steven
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8962542/
https://www.ncbi.nlm.nih.gov/pubmed/35346327
http://dx.doi.org/10.1186/s13059-022-02652-8
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author Emms, David Mark
Kelly, Steven
author_facet Emms, David Mark
Kelly, Steven
author_sort Emms, David Mark
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02652-8.
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spelling pubmed-89625422022-03-30 SHOOT: phylogenetic gene search and ortholog inference Emms, David Mark Kelly, Steven Genome Biol Method 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02652-8. BioMed Central 2022-03-28 /pmc/articles/PMC8962542/ /pubmed/35346327 http://dx.doi.org/10.1186/s13059-022-02652-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Emms, David Mark
Kelly, Steven
SHOOT: phylogenetic gene search and ortholog inference
title SHOOT: phylogenetic gene search and ortholog inference
title_full SHOOT: phylogenetic gene search and ortholog inference
title_fullStr SHOOT: phylogenetic gene search and ortholog inference
title_full_unstemmed SHOOT: phylogenetic gene search and ortholog inference
title_short SHOOT: phylogenetic gene search and ortholog inference
title_sort shoot: phylogenetic gene search and ortholog inference
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8962542/
https://www.ncbi.nlm.nih.gov/pubmed/35346327
http://dx.doi.org/10.1186/s13059-022-02652-8
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