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Nucleic Acids Research 2006 34(Database Issue):D572-D580; doi:10.1093/nar/gkj118
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Nucleic Acids Research, 2006, Vol. 34, Database issue D572-D580
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

TreeFam: a curated database of phylogenetic trees of animal gene families

Heng Li1,2,3, Avril Coghlan4, Jue Ruan1, Lachlan James Coin4, Jean-Karim Hériché4, Lara Osmotherly4, Ruiqiang Li1,5, Tao Liu1, Zhang Zhang1,6, Lars Bolund1,3, Gane Ka-Shu Wong1,7, Weimou Zheng1,2, Paramvir Dehal8, Jun Wang1,3,5 and Richard Durbin4,*

1Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute Beijing 101300, China 2Institute of Theoretical Physics, Chinese Academy of Sciences Beijing 100080, China 3Institute of Human Genetics, University of Aarhus DK-8000 Aarhus C, Denmark 4Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK 5Department of Biochemistry and Molecular Biology, University of Southern Denmark DK-5230 Odense M, Denmark 6Institute of Computing Technology, Chinese Academy of Sciences Beijing 100080, China 7University of Washington Genome Center, Department of Medicine, University of Washington Seattle, WA 98195, USA 8Evolutionary Genomics Department, Department of Energy Joint Genome Institute and Lawrence Berkeley National Laboratory Walnut Creek, California, USA

*To whom correspondence should be addressed. Tel: +44 1223 834244; Fax: +44 1223 494919; Email: rd{at}sanger.ac.uk

Received August 15, 2005. Revised October 19, 2005. Accepted October 19, 2005.

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ~40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

Correspondence may also be addressed to Jun Wang. Tel: +86 10 80481664; Fax: +86 10 80498676; Email: wangj{at}genomics.org.cn

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


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