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.

More at http://phylomedb.org/