ArticleNucleic acids research2014
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers.
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137 citing papers in PubMed.
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- SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.Molecular biology and evolution · 2022Article
- PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.Nucleic acids research · 2022Article
- An overview of online resources for intra-species detection of gene duplications.Frontiers in genetics · 2022Review
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- Updates to HCOP: the HGNC comparison of orthology predictions tool.Briefings in bioinformatics · 2021Article
- Orthology Clusters from Gene Trees with Possvm.Molecular biology and evolution · 2021Article
- Revisiting Shao and Sokal'sJournal of mathematical biology · 2021Article
- FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.Genes · 2021Article
77 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.
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