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

By Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, I. Denisov, Diego J. Kormes, M. Marcet-Houben, Toni Gabaldón. 2010

154 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

The genome of melon (Cucumis melo L.) (2012, unknown): “Huerta-Cepas J, et al. (2011) PhylomeDB v3.”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “Phylogenetic trees were reconstructed using the phylomeDB pipeline described in (61).”
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation (2014, methodology): “…differences define also alternatively what is an orthologous group (i.e. OMA [15], MultiParanoid [16]) or specify orthology after comparing gene family trees with an evolutionary model, such as a species tree (TreeFam [17], EnsEMBL Compara [18], PhylomeDB [19], LOFT [20], Homologene [21]).”