Journal article
SHOOT: phylogenetic gene search and ortholog inference
- 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, 1.8MB, Terms of use)
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- Publisher copy:
- 10.1186/s13059-022-02652-8
Authors
- Publisher:
- BioMed Central
- Journal:
- Genome Biology More from this journal
- Volume:
- 23
- Article number:
- 85
- Publication date:
- 2022-03-28
- Acceptance date:
- 2022-03-08
- DOI:
- EISSN:
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1474-760X
- ISSN:
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1474-7596
- Pmid:
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35346327
- Language:
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English
- Keywords:
- Pubs id:
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1248925
- Local pid:
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pubs:1248925
- Deposit date:
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2022-05-26
Terms of use
- Copyright holder:
- Emms and Kelly
- Copyright date:
- 2022
- Rights statement:
- Copyright © 2022 The Author(s). This 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/. The Creative Commons Public Domain Dedication waiver (http://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.
- Licence:
- CC Attribution (CC BY)
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