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- Title
TreeFam: 2008 Update.
- Authors
Ruan, Jue; Li, Heng; Chen, Zhongzhong; Coghlan, Avril; Coin, Lachlan James M; Guo, Yiran; Hériché, Jean-Karim; Hu, Yafeng; Kristiansen, Karsten; Li, Ruiqiang; Liu, Tao; Moses, Alan; Qin, Junjie; Vang, Søren; Vilella, Albert J; Ureta-Vidal, Abel; Bolund, Lars; Wang, Jun; Durbin, Richard
- 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.
- Publication
Nucleic acids research, 2008, Vol 36, Issue Database issue, pD735
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gkm1005