TreeFam: a curated database of phylogenetic trees of animal gene families
Open accessAbstract
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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TreeFam identified 13,810 homologous gene families shared by yak, cattle, human and dog.
“First, we used TreeFam 20 to identify 13,810 homologous gene families shared by 4 species (yak, cattle, human and dog):”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [20]
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- Authors
- Li, H.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Li, H.
- ORCID
- Li, H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-01
- Volume
- 34
- Issue
- 90001
- Pages
- D572-D580
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1347480
- OpenAlex
- W2137084536
- Cited by
- 523
- References
- 53
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 15 · 2023: 20 · 2022: 27 · 2021: 33 · 2020: 32 · 2019: 26 · 2018: 29 · 2017: 19 · 2016: 23 · 2015: 28 · 2014: 30 · 2013: 36 · 2012: 26
- FWCI
- 8.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-AC03-?, AC03-76SF00098, DEAC03-76SF00098)
- Wellcome Trust
- European Commission (LSHG-CT-2004-503464, DE-AC03-76SF00098)
- National Natural Science Foundation of China (90403110, 90403130)
- Biological and Environmental Research
- Lawrence Berkeley National Laboratory (DE AC03 76SF00098)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- phylogenetic tree, orthologs, paralogs, gene family evolution, curated database, animal genomes, protein evolution
- MeSH terms
- Animals, Genes, Humans, Phylogeny, Proteins, Software, User-Computer Interface, Evolution, Molecular, Internet, Genomics, Databases, Genetic, Mice, Rats
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