PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies

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Abstract

PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.

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Author and article information

Contributors

Diego Fuentes

Manuel Molina

Uciel Chorostecki:

ORCID: https://orcid.org/0000-0003-2229-6853

Salvador Capella-Gutiérrez:

ORCID: https://orcid.org/0000-0002-0309-604X

Marina Marcet-Houben

Toni Gabaldón:

ORCID: https://orcid.org/0000-0003-0019-1735

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 07 January 2022

Publication date (Electronic): 30 October 2021

Publication date PMC-release: 30 October 2021

Volume: 50

Issue: D1

Pages: D1062-D1068