BUCKy: A program for Bayesian Concordance Analysis

Introduction

BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Instead, groups of genes sharing the same tree are detected (while accounting for uncertainty in gene tree estimates), and then combined to gain more resolution on their common tree. No assumption is made regarding the reason for discordance among gene trees.

If you use BUCKy for research, please cite:

C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426. Abstract and Erratum.

Another great reading:
David Baum. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56(2):417-426 abstract

Downloads

Follow the links below to download the program, either the source code if you wish to compile on your own machine, or executable files.

Version Source, including
examples and manual		 Binaries Manual
1.2b (12/2008) tarball executable files pdf
1.3.0 (1/2009) tarball executable files pdf
1.3.1 (10/2009) tarball   pdf
developement version (most recent is 1.3.1)    

For those who wish, you can get the latest version from this git repository.

Here are the slides used for a demo of the program, at the workshop "Estimating Species Tree" (University of Michigan, Jan. 2009).

Choice of a priori discordance parameter

An interactive website that shows graphs of the prior distribution for the number of distinct groups.

Version history

Version 1.3.1 can handle any number of taxa. mbsum was improved to be more flexible with line breaks and taxon numbers.

Version 1.3.0 includes the possibility to indicate the names of input files (one input file per gene) into a single file, and the use of translate tables to check that all genes use the same ordering of taxa.

Version 1.2b includes multiple independent runs and a bug fix regarding the group update.

Version 1.1 can be found here.

Last modified: Thu Oct 29 13:59:53 CDT 2009