title: TreeFam: a curated database of phylogenetic trees of animal gene families.
abstract: 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; approximately 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.
authors.affiliation: Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Avril
authors.initials: A
authors.lastname: Coghlan
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.forename: Lachlan James
authors.initials: LJ
authors.lastname: Coin
authors.forename: Jean-Karim
authors.initials: JK
authors.lastname: Hériché
authors.forename: Lara
authors.initials: L
authors.lastname: Osmotherly
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Weimou
authors.initials: W
authors.lastname: Zheng
authors.forename: Paramvir
authors.initials: P
authors.lastname: Dehal
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005796:Genes; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D010802:Phylogeny; D011506:Proteins / Q000145:classification* / Q000235:genetics; D051381:Rats; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins