PhylomeDB

PhylomeDB
Name	PhylomeDB
URL	phylomedb.org
Contact	tgabaldon@crg.eu
Data_types	Genome data, Comparative genomics data
Resources/Tools	Multisequence alignment, Query tool, Downloads

PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes , including Maximum Likelihood or Bayesian tree inference, alignment trimming and evolutionary model testing. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions.

Reference

Huerta-Cepas et al.: PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res. 2011;39:D556-60. PMID: 21075798. DOI.