PhylomeDB is a public biological database for complete catalogs 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 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, 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, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and interactive tree image.
New steps on phylomeDB.
The tree searching engine of PhylomeDB was updated to provide a gene-centric view of all phylomeDB resources. Thus, after a protein or gene search, all the available trees in phylomeDB are listed and organized by phylome and tree type. Users can switch among all available seed and collateral trees without missing the focus on the searched protein or gene.
In phylomeDB v4 all the information available for each tree is now shown using an integrated layout in which tree topology, taxonomy data, alignments and domain annotations, and event-age (phylostratigraphy) information are rendered in the same figure using the newest visualization features provided by the ETE toolkit v2.2:
Also, users can download relevant data, including the whole database, a specific phylome or, from the tree entry page, the relevant data corresponding to that tree. In this new release we have implemented the possibility to download orthology predictions from a tree in the recently developed OrthoXML standard format, in addition to a tabulated format.
Quest for Orthologs.
The Quest for Orthologs (QfO) consortium involve more than 30 phylogenomic databases. The main of the consortium is improve and standardize orthology predictions through collaboration and discuss about new emerging methods.