BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. 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/.
Keywords for this software
References in zbMATH (referenced in 7 articles )
Showing results 1 to 7 of 7.
- Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
- Allman, Elizabeth S.; Degnan, James H.; Rhodes, John A.: Split probabilities and species tree inference under the multispecies coalescent model (2018)
- Skwerer, Sean; Provan, Scott; Marron, J. S.: Relative optimality conditions and algorithms for treespace Fréchet means (2018)
- Roch, Sebastien; Steel, Mike: Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent (2015)
- Warnow, Tandy: Large-scale multiple sequence alignment and phylogeny estimation (2013)
- Degnan, James H.; Rosenberg, Noah A.; Stadler, Tanja: The probability distribution of ranked gene trees on a species tree (2012)
- Allman, Elizabeth S.; Degnan, James H.; Rhodes, John A.: Determining species tree topologies from clade probabilities under the coalescent (2011)