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2010•BioinformaticsRequires access

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

Bret R. Larget, Satish K. Kotha, Colin N. Dewey, Cécile Ané

Open publisher page 466 citations

Abstract

Abstract Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. Availability: BUCKy is open source and distributed under the GNU general public license at www.stat.wisc.edu/∼ane/bucky/. Contact: ane@stat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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What this paper is about

Abstract Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. Availability: BUCKy is open source and distributed under the GNU general public license at www.stat.wisc.edu/∼ane/bucky/. Contact: ane@stat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Available abstract

Abstract Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. Availability: BUCKy is open source and distributed under the GNU general public license at www.stat.wisc.edu/∼ane/bucky/. Contact: ane@stat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Key concepts: Concordance, Coalescent theory, Population, Tree (set theory), Phylogenetic tree, Clade, Cluster analysis, Computer science

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