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TreeFam: 2008 Update

By Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Heacute, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang and Richard Durbin


TreeFam 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

Topics: Genetics, 1311 Genetics
Publisher: 'Oxford University Press (OUP)'
Year: 2008
DOI identifier: 10.1093/nar/gkm1005
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