Welcome to PhylomeDB 4!

PhylomeDB is a public 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 faciliates 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. 

What's new in phylomeDB 4?


Latest story

Mon, 05/19/2014 - 11:01

Arxula adeninivorans (Blastobotrys adeninivorans) is a dimorphic yeast with unusual characteristics that make it of great biotechnological interest. It is not only a source of many enzymes with interesting properties such as glucoamylase, tannase, lipasses and phosphatases, but it is also a useful yeast for the heterologous expression of proteins. In addition, this yeast is thermotolerant, xerotolerant and osmotolerant, which makes it a great model to study such phenotypic adaptations. In the context of the sequencing effort of this genome, we reconstructed the phylome for this species. This served to resolve the phylogenetic relationships with other sequenced yeasts but also to detect patterns of gene family expansions, which unveiled past multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not...

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