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, 09/15/2014 - 21:09

 PhylomeDB extends its repertoire of fungal phylomes with that of a genome of a poorly sample clade, that of the basal group zygomycetes. In this case the phylome (245) of the human pathogenic mucorales Lichtemia corymbifera has served to reveal extensive past gene duplications in this group. Lichtheimia species are the second most important cause of mucormycosis in Europe. The sequencing of its genome and the comparison with other Zygomycete species, particularly of Rhizopus delemar, the main cause of mucormycosis in Europe, has revealed specific adaptations in each of the lineages. Lichteimia, presents a high number of gene duplications that are attributable to segmental duplications. The availability of the phylome has enabled to trace and provide a relative timing of the duplications events in this group. You can browse the phylome and find more information in the associated publication:

Schwartze et. al. 2014. Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary...

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