PhylomeDB v3.0

It is a public database for genome-wide collections of gene phylogenies (phylomes). It is also a major source for phylogeny-based orthology and paralogy predictions. 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.

Topic

Phylogeny;Phylogenomics;Pathology;Model organisms

Detail

  • Operation: Tree-based sequence alignment;Gene prediction;Phylogenetic tree reconstruction;Phylogenetic species tree construction

  • Software interface: Database portal

  • Language: -

  • License: -

  • Cost: -

  • Version name: -

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

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  • Output: -

  • Contact: tgabaldon@crg.es

  • Collection: -

  • Maturity: -

Publications

  • PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
  • Huerta-Cepas J, et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. 2011; 39:D556-60. doi: 10.1093/nar/gkq1109
  • https://doi.org/10.1093/nar/gkq1109
  • PMID: 21075798
  • PMC: PMC3013701

Download and documentation

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