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Nucleic acids research
Jan 01, 2006;34 (Database issue): D572-80.

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

Heng Li, Avril Coghlan, Jue Ruan, Lachlan James Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Weimou Zheng, Paramvir Dehal, Jun Wang, Richard Durbin
Author Information
  1. Heng Li: Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China.
PMID: 16381935 DOI: 10.1093/nar/gkj118

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.

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Grants

  1. /Wellcome Trust

MeSH Term

Animals
Databases, Genetic
Evolution, Molecular
Genes
Genomics
Humans
Internet
Mice
Phylogeny
Proteins
Rats
Software
User-Computer Interface

Chemicals

Proteins
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Links to CNCB-NGDC Resources

Database Commons: DBC000274 (TreeFam)

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