HOME BROWSE PHYLOMES DOWNLOADS FAQ HELP ABOUT
Search! Blast Search! Select phylomes
PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users tointeractively 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 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.
Comparative Genomics Group at CRG (Barcelona, Spain). | Citation
http://phylomedb.org/help/doku.php
User's Manual FAQ About How to cite Go to PhylomeDB!
The complete collection of evolutionary histories of all genes in a genome, the so-called phylome, constitutes a valuable source of information. Traditionally prevented by large demands on time and computer power, the reconstruction of phylomes is now feasible thanks to recent developments in computers and algorithms. In order to provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein.
You can find the different sections of this manual using this index: