CAFE: a computational tool for the study of gene family evolution
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Summary: We present CAFE (Computational Analysis of gene Family Evolution), a tool for the statistical analysis of the evolution of the size of gene families. It uses a stochastic birth and death process to model the evolution of gene family sizes over a phylogeny. For a specified phylogenetic tree, and given the gene family sizes in the extant species, CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss (quantified by a p-value) and identify which branches cause the p-value to be small for significant families. Availability: Software is available from Contact: mwh@indiana.edu
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Six of these 621 orthogroups show evidence of gene family expansion and contraction within Danio as detected by CAFÉ.
“Six of these 621 orthogroups show evidence of gene family expansion and contraction within Danio as detected by CAFÉ43.”
From Genomic and genetic insights into speciation and pigment pattern diversification in <i>Danio</i> fishes (2025) · cites this paper as [43]
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- Authors
- De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W.
- Affiliations
- K.U.Leuven, OKP Research Group 1 1 Tiensestraat 102, 3000 Leuven, Belgium
- University of California, Davis (US)
- Indiana University Bloomington (US)
- Corresponding author
- Hahn, Matthew W.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-03-16
- Volume
- 22
- Issue
- 10
- Pages
- 1269-1271
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2122821321
- Cited by
- 1,790
- References
- 0
- Citations by year
- 2026: 127 · 2025: 167 · 2024: 189 · 2023: 212 · 2022: 284 · 2021: 269 · 2020: 182 · 2019: 88 · 2018: 54 · 2017: 31 · 2016: 37 · 2015: 26 · 2014: 29 · 2013: 18 · 2012: 21
- FWCI
- 3.40
- Type
- journal article
- Language
- en
- Open access
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Explore Bristol Research (submittedVersion)
- Funders
- National Science Foundation (0528465)
- National Institutes of Health
- National Human Genome Research Institute (R33HG003070)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- gene family evolution, gene family size, birth-death processes, phylogenetic tree, gene gain and loss, stochastic modeling, gene family expansion and contraction
- MeSH terms
- Algorithms, Chromosome Mapping, DNA Mutational Analysis, Multigene Family, Phylogeny, Software, User-Computer Interface, Genetic Variation, Evolution, Molecular
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