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.
B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis. Bioinformatics (advance access). pdf
Another great reading:
David Baum. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56(2):417-426 abstract