CAFE: a computational tool for the study of gene family evolution

By Tijl De Bie, Nello Cristianini, Jeffery P. Demuth, Matthew W. Hahn. Bioinform., 2006

1,557 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4de8c7698c38f4231d03df7a5817d590b3a954ce

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Stephen Fitzgerald
2. Javier Herrero
3. Kathryn M Beal
4. Albert J. Vilella
5. Bernard Henrissat
6. A. Kohler
7. Francis Martin
8. Edward L. Braun

In Molecular Biology

1. Bernard Henrissat
2. Francis Martin
3. Vincent Lombard
4. A. Kohler
5. Pedro M. Coutinho
6. Paul Flicek
7. Stephen Fitzgerald
8. Leo Gordon

Citations in the corpus

• Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, methodology): “To better understand the role of these enzymes in wood-decaying basidiomycetes, we used the CAFE program (34) to explore their evolution according to a stochastic model of gene death and birth.”
• Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “As input for the CAFE 3 program (134, 135), we used ultrametric trees based on the well-resolved phylogenies of birds (the TENT tree in (5)) and eutherian mammals (136).”
• The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, methodology): “The CAFÉ program (48) was used to analyze gene family expansions and contractions in the 27 families of CAZymes and oxidoreductases listed above, as well as in carbohydrate binding modules (CBM1) associated with eleven CAZyme families (see below).”
• Genome sequence of the cultivated cotton Gossypium arboreum (2014, positive): “CAFE 66 was used to predict the expansion and contraction of gene numbers on the basis of the topological gene tree.”
• Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, methodology): “Multigene families were analyzed for evolutionary changes in protein family size using the CAFE program (36) (Fig.”
• Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. (2013, background): “…across multiple species and an ultrametric phylogenetic tree describing relationships among these species, the original CAFE software package (De Bie et al. 2006) can estimate the maximum likelihood value of the rate parameter, l , and the maximum likelihood estimates (MLEs) of the size of each…”
• Mutations in smooth muscle α-actin (ACTA2) lead to thoracic aortic aneurysms and dissections (2007, methodology): “Using the EM algorithm implemented by the CAFE softwar”
• Ensembl comparative genomics resources (2016, methodology): “Gene gains and losses in each GeneTree are calculated by starting from the number of gene copies in each species and using CAFE (42) to estimate how many genes existed in each lineage before a speciation event.”
• Ensembl comparative genomics resources (2016, methodology): “Gene gains and losses in each GeneTree are calculated by starting from the number of gene copies in each species and using CAFE (42) to estimate how many genes existed in each lineage before a speciation event.”