BEST is a free phylogenetics program written by Liang Liu to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication. The program works within the popular Bayesian phylogenetics package MrBayes (Ronquist and Huelsenbeck, Bioinformatics, 2003). BEST parameters are defined using the prset command in MrBayes.
If you publish research that uses best you have to cite it:
BEST references (by date of publication).
Liu. Reconstructing posterior distributions of a species phylogeny using estimated gene tree distributions. Ph.D. Dissertation. The Ohio State University. 2006.
Liu and Pearl. Species Trees from Gene Trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 56: 504-514, 2007.
Edwards, Liu, and Pearl. High resolution species trees without concatenation. PNAS, 104:5936-5941, 2007.
Edwards, Liu, and Pearl. High resolution species trees without concatenation: Supplemental Material. PNAS, 2007.
Liu, Pearl, Brumfield, and Edwards. Estimating species trees using multiple allele data. Evolution,62:2080-2091, 2008.
Liu. BEST: Bayesian estimation of species trees under the coalescent model.Bioinformatics, 24:2542-2543, 2008.