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Spanish Ministry of Science (GEN2006-27784-E/PAT, BFU2009-09168). Funding for open access charge: CRG, Spanish Ministry of Science and Innovation.

Analysis of institutional authors

Huerta-Cepas, JaimeAuthorCapella-Gutierrez, SalvadorAuthorPryszcz, Leszek P.AuthorDenisov, IvanAuthorKormes, DiegoAuthorMarcet-Houben, MarinaAuthorGabaldon, ToniCorresponding Author

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June 15, 2019
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PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

Publicated to:Nucleic Acids Research. 39 D556-D560 - 2011-01-01 39(), DOI: 10.1093/nar/gkq1109

Authors: Huerta-Cepas, J; Capella-Gutierrez, S; Pryszcz, LP; Denisov, I; Kormes, D; Marcet-Houben, M; Gabaldón, T

Affiliations

Ctr Regulacio Genom, Bioinformat & Genom Programme, Barcelona 08003, Spain - Author

Abstract

The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416 093 trees and 165 840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic access. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana, but also alternative model species such as the human pathogen Candida albicans, or the pea aphid Acyrtosiphon pisum. Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights.

Keywords

DatabaseEvolutionGenesMultiple sequence alignmentReconstruction

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nucleic Acids Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2011, it was in position 26/290, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 10.58, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-07, the following number of citations:

  • WoS: 118
  • Scopus: 116
  • Europe PMC: 101

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-07:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 189.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 191 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 3.
  • The number of mentions on Wikipedia: 2 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (HUERTA CEPAS, JAIME) and Last Author (Gabaldon Esteban, Toni).

the author responsible for correspondence tasks has been Gabaldon Esteban, Toni.