PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
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Cita com:
hdl:2117/356203
Tipus de documentArticle
Data publicació2021
EditorOxford University Press
Condicions d'accésAccés obert
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continguts d'aquesta obra estan subjectes a la llicència de Creative Commons
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Reconeixement-NoComercial 3.0 Espanya
ProjecteRETVOLUTION - Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes. (EC-H2020-724173)
MULTI_FOLDS - Not one but many: adopting structural flexibility in the analysis of the evolution of lncRNAs. (EC-H2020-793699)
MULTI_FOLDS - Not one but many: adopting structural flexibility in the analysis of the evolution of lncRNAs. (EC-H2020-793699)
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.
Dataset
http://phylomedb.org/
CitacióFuentes, D. [et al.]. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. "Nucleic Acids Research", 2021, gkab966.
ISSN1362-4962
0305-1048
0305-1048
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gkab966.pdf | 1,601Mb | Visualitza/Obre |