TreeFam and Ensembl: Phylogenetic resources

The Ensembl and Ensembl Genomes projects create and distribute genome annotations for a wide range of genomes, including model organisms. The number of publicly available genomes is increasingly rapidly, providing an opportunity for new insights via comparative genomics. TreeFam produces phylogenetic trees and orthology predictions, though previously only for metazoans. Here we describe advances in TreeFam, targeted to achieve scalability to all Ensembl eukaryotes. The key component is a new library of HMM (Hidden Markov Model) profiles (Figure 2) that was created from Panther and TreeFam, with custom profiles to fill gaps in gene coverage. The library represents gene families across all eukaryotes.