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...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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BioMed Central
2022
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| _version_ | 1826307805130260480 |
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| author | Emms, DM Kelly, S |
| author_facet | Emms, DM Kelly, S |
| author_sort | Emms, DM |
| collection | OXFORD |
| 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.
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| first_indexed | 2024-03-07T07:08:35Z |
| format | Journal article |
| id | oxford-uuid:f60c8b9c-8022-4264-b33d-b20e60cc2586 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:08:35Z |
| publishDate | 2022 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:f60c8b9c-8022-4264-b33d-b20e60cc25862022-05-27T06:32:36ZSHOOT: phylogenetic gene search and ortholog inferenceJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f60c8b9c-8022-4264-b33d-b20e60cc2586EnglishSymplectic ElementsBioMed Central2022Emms, DMKelly, SDetermining 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. |
| spellingShingle | Emms, DM Kelly, S 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 |
| work_keys_str_mv | AT emmsdm shootphylogeneticgenesearchandorthologinference AT kellys shootphylogeneticgenesearchandorthologinference |