PhylomeDB is a public database for complete collections of gene phylogenies (phylomes).
Users can 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 inference, alignment trimming and evolutionary model testing. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions.
PhylomeDB uses metaPhOrs (meta-Phylogeny based Orthologs) as a method for predicting orthologs and paralogs. metaPhOrs combines resources of several databases (PhylomeDB, EnsemblCompara, EggNOG, OrthoMCL, COG, Fungal Orthogroups, and TreeFam) to test robustness of each prediction.
All PhylomeDB resources are also accessible through ETE2: a Python Environment for phylogenetic Tree Exploration.