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

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...

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Autores principales: Huerta-Cepas, Jaime, Capella-Gutierrez, Salvador, Pryszcz, Leszek P., Denisov, Ivan, Kormes, Diego, Marcet-Houben, Marina, Gabaldón, Toni
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013701/
https://www.ncbi.nlm.nih.gov/pubmed/21075798
http://dx.doi.org/10.1093/nar/gkq1109
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author Huerta-Cepas, Jaime
Capella-Gutierrez, Salvador
Pryszcz, Leszek P.
Denisov, Ivan
Kormes, Diego
Marcet-Houben, Marina
Gabaldón, Toni
author_facet Huerta-Cepas, Jaime
Capella-Gutierrez, Salvador
Pryszcz, Leszek P.
Denisov, Ivan
Kormes, Diego
Marcet-Houben, Marina
Gabaldón, Toni
author_sort Huerta-Cepas, Jaime
collection PubMed
description 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.
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spelling pubmed-30137012011-01-03 PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions Huerta-Cepas, Jaime Capella-Gutierrez, Salvador Pryszcz, Leszek P. Denisov, Ivan Kormes, Diego Marcet-Houben, Marina Gabaldón, Toni Nucleic Acids Res Articles 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. Oxford University Press 2011-01 2010-11-11 /pmc/articles/PMC3013701/ /pubmed/21075798 http://dx.doi.org/10.1093/nar/gkq1109 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Huerta-Cepas, Jaime
Capella-Gutierrez, Salvador
Pryszcz, Leszek P.
Denisov, Ivan
Kormes, Diego
Marcet-Houben, Marina
Gabaldón, Toni
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title_full PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title_fullStr PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title_full_unstemmed PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title_short PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
title_sort phylomedb v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013701/
https://www.ncbi.nlm.nih.gov/pubmed/21075798
http://dx.doi.org/10.1093/nar/gkq1109
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