OrthoFinder: phylogenetic orthology inference for comparative genomics
| Autor: | Emms, David M., Kelly, Steven |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Gene duplication lcsh:QH426-470 Phylogenetic inference Computer science Ortholog inference Inference Computational biology Biology 010603 evolutionary biology 01 natural sciences Homology (biology) 03 medical and health sciences Animals Gene lcsh:QH301-705.5 Phylogeny 030304 developmental biology Comparative genomics 0303 health sciences Gene tree inference Phylogenetic tree Heuristic Genomics lcsh:Genetics Tree (data structure) lcsh:Biology (General) Scalability Benchmark (computing) Algorithms Software 010606 plant biology & botany |
| Zdroj: | Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019) Genome Biology |
| ISSN: | 1474-760X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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