TreeFam: 2008 Update

Jue Ruan(University of Southern Denmark), Heng Li(Wellcome Sanger Institute), Zhongzhong Chen(European Bioinformatics Institute), Avril Coghlan(BGI Group (China)), Lachlan Coin(Beijing Institute of Genomics), Yong Guo(Beijing Institute of Genomics), Jean-Karim Hèriché(BGI Group (China)), Yu‐Chen Hu(Aarhus University Hospital), Karsten Kristiansen(Wellcome Sanger Institute), Rong Li(European Bioinformatics Institute), T. Liu(European Bioinformatics Institute), A. Moses(Aarhus University Hospital), Junjie Qin(BGI Group (China)), Søren Vang(BGI Group (China)), Albert J. Vilella(European Bioinformatics Institute), A. Ureta-Vidal(University of Southern Denmark), Lars Bolund(Aarhus University Hospital), Jian Wang(BGI Group (China)), Richard Durbin(University of Southern Denmark)
Nucleic Acids Research
December 2, 2007
10.1093/nar/gkm1005
Cited by 345Open Access
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Abstract

TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14,351 families. We have expanded TreeFam to include 25 fully sequenced animal genomes, as well as four genomes from plant and fungal outgroup species. We have also introduced more accurate approaches for automatically grouping genes into families, for building phylogenetic trees, and for inferring orthologues and paralogues. The user interface for viewing phylogenetic trees and family information has been improved. Furthermore, a new perl API lets users easily extract data from the TreeFam mysql database.

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