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Cited by 217Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksChromosomal and Genetic Variations

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

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Huerta-Cepas, Jaime, Capella-Gutiérrez, Salvador, Pryszcz, Leszek P., Marcet-Houben, Marina, Gabaldón, Toni·2014·Nucleic Acids Research
DOI 10.1093/nar/gkt1177PMC PMC3964985
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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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  • Gene tree-based methods determine whether the evolutionary lineages of two genes coalesce in a speciation or a duplication node.

    “Gene tree-based methods determine whether the evolutionary lineages of two genes coalesce in a speciation or a duplication node (12–14).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [13]

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Authors
Huerta-Cepas, J., Capella-Gutiérrez, S., Pryszcz, L. P., Marcet-Houben, M., & Gabaldón, T.
Affiliations
Institució Catalana de Recerca i Estudis Avançats (ES)
Corresponding author
Gabaldón, Toni
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2013-11-25
Volume
42
Issue
D1
Pages
D897-D902
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkt1177
PMC
PMC3964985
OpenAlex
W2114676910
Cited by
217
References
1
Citations by year
2026: 2 · 2025: 3 · 2024: 4 · 2023: 4 · 2022: 10 · 2021: 20 · 2020: 26 · 2019: 28 · 2018: 24 · 2017: 29 · 2016: 31 · 2015: 26 · 2014: 9 · 2012: 1
FWCI
8.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
Funders
  • European Commission (2007–2013, FP/2007/2013)
  • Fonds National de la Recherche Luxembourg
  • Ministerio de Economía y Competitividad (BIO2012-37161)
  • Qatar National Research Fund (5-298-3-086, NPRP 5‐298‐3‐086, NPRP-5)
  • FP7 Ideas: European Research Council (310325)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
phylogenetic tree, orthology prediction, paralogy, gene family evolution, horizontal gene transfer, incomplete lineage sorting, protein domain annotation, genome annotation, transcriptome annotation, phylogenomics
MeSH terms
Humans, Phylogeny, Proteins, Genome, Internet, Proteome, Gene Expression Profiling, Databases, Genetic

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