OrthoFinder: phylogenetic orthology inference for comparative genomics

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmark...

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Vydané v:Genome Biology Ročník 20; číslo 1; s. 238
Hlavní autori: Emms, David M., Kelly, Steven
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 14.11.2019
Springer Nature B.V
BMC
Predmet:
Accuracy
Algorithms
Animal Genetics and Genomics
Animals
Automation
Bioinformatics
Biological research
Biomedical and Life Sciences
Comparative genomics
data collection
Evolution
Evolutionary Biology
Gene duplication
Gene tree inference
Genes
Genomics
Genomics - methods
Heuristic
Human Genetics
Life Sciences
Methods
Microbial Genetics and Genomics
Online data bases
Ortholog inference
Orthology
Phylogenetics
Phylogeny
Plant Genetics and Genomics
Software
Software utilities
Statistical analysis
statistics
Trees
Ortholog inference
Comparative genomics
Gene tree inference
Gene duplication
ISSN:1474-760X, 1474-7596, 1474-760X
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Popis
Shrnutí:Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1832-y