SHOOT: phylogenetic gene search and ortholog inference

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...

Full description

Bibliographic Details
Main Authors: Emms, D.M (Author), Kelly, S. (Author)
Format: Article
Language:English
Published: BioMed Central Ltd 2022
Subjects:
algorithm
Algorithms
article
Biological Evolution
evolution
orthology
Orthology inference
phylogenetic tree
Phylogenetic tree inference
phylogeny
Phylogeny
Sequence similarity search
shoot
velocity
Online Access:View Fulltext in Publisher
Description
Summary: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. © 2022, The Author(s).
ISBN:14747596 (ISSN)
DOI:10.1186/s13059-022-02652-8

Similar Items