期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 38, 期 11, 页码 5204-5208出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msab234
关键词
orthology inference; gene phylogenetics; comparative genomics
资金
- European Research Council (ERC) under the European Union [851647]
- Spanish Ministry of Science and Innovation [PGC2018-098210-A-I00]
- Centro de Excelencia Severo Ochoa scheme [SEV-2016-0571]
- Agencia Estatal de Investigacion
- Juan de la Cierva fellowship from the Spanish Ministry of Economy, Industry, and Competitiveness [FJC2018-036282-I]
- European Research Council (ERC) [851647] Funding Source: European Research Council (ERC)
Possvm is a tool that automates the identification of orthologous gene clusters and classification of gene families with high precision and recall. It uses the species overlap algorithm and MCL algorithm to achieve this, providing reusable outputs and phylogeny-aware gene annotations.
Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL [Markov clustering algorithm]) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and classifying gene families. It identifies orthology relationships between genes using the species overlap algorithm to infer taxonomic information from the gene tree topology, and then uses the MCL to identify orthology clusters and provide annotated gene families. Our benchmarking shows that this approach, when provided with accurate phylogenies, is able to identify manually curated orthogroups with very high precision and recall. Overall, Possvm automates the routine process of gene tree inspection and annotation in a highly interpretable manner, and provides reusable outputs and phylogeny-aware gene annotations that can be used to inform comparative genomics and gene family evolution analyses.
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