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Literature DB >> 20861028

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.

Bret R Larget¹, Satish K Kotha, Colin N Dewey, Cécile Ané.

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/.

Mesh：

Year: 2010 PMID： 20861028 DOI： 10.1093/bioinformatics/btq539

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

116 in total

1. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

Authors: David W Weisrock; Stacey D Smith; Lauren M Chan; Karla Biebouw; Peter M Kappeler; Anne D Yoder
Journal: Mol Biol Evol Date: 2012-01-12 Impact factor: 16.240

2. Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods.

Authors: Dayana E Salas-Leiva; Alan W Meerow; Michael Calonje; M Patrick Griffith; Javier Francisco-Ortega; Kyoko Nakamura; Dennis W Stevenson; Carl E Lewis; Sandra Namoff
Journal: Ann Bot Date: 2013-08-29 Impact factor: 4.357

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.

1. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

2. Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods.

3. Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.

4. A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes.

5. PRANC: ML species tree estimation from the ranked gene trees under coalescence.

6. Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae).

7. Modeling Hybridization Under the Network Multispecies Coalescent.

8. The estimation of tree posterior probabilities using conditional clade probability distributions.

9. BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.

10. Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.