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

Bie Tijl De; Nello Cristianini; Demuth Jeffery P.; Hahn Matthew W.; Editor Associate; Stoeckert Chris

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

Bie Tijl De, Nello Cristianini, Demuth Jeffery P., Hahn Matthew W., Editor Associate, Stoeckert Chris

Research output: Chapter in Book/Report/Conference proceeding › Conference Contribution (Conference Proceeding)

Abstract

Summary:We present CAFEC omputational 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 http:www.bio.indiana.edu hahnlabSoftware.html Contact: [email protected]

Translated title of the contribution	Genome analysis CAFE: a computational tool for the study of gene family evolution
Original language	English
Title of host publication	Unknown
Publication status	Published - 2007

Bibliographical note

Other page information: 1269-1271
Other identifier: 2000801

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@inproceedings{bb62fc049ca048e3a594f9db15db8745,

title = "Genome analysis CAFE: a computational tool for the study of gene family evolution",

abstract = "Summary:We present CAFEC omputational 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 http:www.bio.indiana.edu hahnlabSoftware.html Contact: [email protected]",

author = "{Tijl De}, Bie and Nello Cristianini and {Jeffery P.}, Demuth and {Matthew W.}, Hahn and Editor Associate and Stoeckert Chris",

note = "Other page information: 1269-1271 Other identifier: 2000801",

year = "2007",

language = "English",

booktitle = "Unknown",

}

TY - GEN

T1 - Genome analysis CAFE: a computational tool for the study of gene family evolution

AU - Tijl De, Bie

AU - Cristianini, Nello

AU - Jeffery P., Demuth

AU - Matthew W., Hahn

AU - Associate, Editor

AU - Chris, Stoeckert

N1 - Other page information: 1269-1271 Other identifier: 2000801

PY - 2007

Y1 - 2007

N2 - Summary:We present CAFEC omputational 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 http:www.bio.indiana.edu hahnlabSoftware.html Contact: [email protected]

AB - Summary:We present CAFEC omputational 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 http:www.bio.indiana.edu hahnlabSoftware.html Contact: [email protected]

M3 - Conference Contribution (Conference Proceeding)

BT - Unknown

ER -

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

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