PhylomeDB
PhylomeDB is a public biological database for complete catalogs of gene phylogenies (phylomes).[1][2][3] 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 tree inference, alignment trimming [4] and evolutionary model testing.
PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that facilitates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit,[5] which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and interactive tree image.