PhylomeDB: a database for genome-wide collections of gene phylogenies

TitlePhylomeDB: a database for genome-wide collections of gene phylogenies
Publication TypeJournal Article
Year of Publication2008
AuthorsHuerta-Cepas, J, Bueno, A, Dopazo, J, Gabaldón, T
JournalNucleic Acids Res
KeywordsAncient Humans *Phylogeny Proteins/classification/genetics Saccharomyces cerevisiae/classification/genetics Sequence Alignment; Base Sequence Escherichia coli/classification/genetics Genes *Genomics History

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. 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. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at


Huerta-Cepas, Jaime Bueno, Anibal Dopazo, Joaquin Gabaldon, Toni Historical Article Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. Epub 2007 Oct 25.