TreeFam v9: a new website, more species and orthology-on-the-fly.

TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15,736 families covering ∼2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI.