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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 ...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1186/s13059-022-02652-8

Authors


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Role:
Author
ORCID:
0000-0002-9065-8978
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Institution:
University of Oxford
Division:
MPLS
Department:
Plant Sciences
Oxford college:
Queen's College
Role:
Author
ORCID:
0000-0001-8583-5362
Royal Society More from this funder
Publisher:
BioMed Central Publisher's website
Journal:
Genome Biology Journal website
Volume:
23
Article number:
85
Publication date:
2022-03-28
Acceptance date:
2022-03-08
DOI:
EISSN:
1474-760X
ISSN:
1474-7596
Pmid:
35346327
Language:
English
Keywords:
Pubs id:
1248925
Local pid:
pubs:1248925
Deposit date:
2022-05-26

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