Bayesian Estimation of Species Trees


DEB 743330 & 743616

Download BEST version 3.0

BEST version 3.0 is avaiable at

Download version 2.3.1

(Updated: January 31, 2010)

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Release Notes

Source Code

BEST (version 2.3) is the source code for Liang Liu's new algorithm that estimates the posterior joint distribution of Gene trees and the posterior distribution of the species tree jointly in one MCMC algorithm. This code works as a modification of the popular phylogenetics software package MrBayes (Ronquist and Huelsenbeck, Bioinformatics, 2003). BEST parameters are defined using the prset command in MrBayes.


Windows: Executable for the Windows version of BEST estimating posterior distribution of gene trees and species trees jointly.

Mac OS X ( Executable for the Macintosh version of BEST estimating posterior distributions of gene trees and species tree jointly. (Note - users have reported a bug in the executable. After unzipping, double clicking the icon will open your terminal program for command line usage, however the program loses track of the directory it is located in and you must specify full file names, including the directory, for commands such as execute and sumt. To avoid the probelm, open your terminal program first and run the executable from there.)

GUI Betas: Mac and Windows executables with a simple user interface are now available in beta version. Open .txt or .nex files then change or fill-in MrBayes and BEST parameters and run the MCMC and view summaries within the interface.


BEST version 2.2 is also available for use on the BioHPC compute cluster at the Computational Biology Service Unit at Cornell University. Go to to run BEST using this resource.

Version history
version # date comment
1.1 - 1.4 August 2004 single allele case only
1.5 October 2006 multiple allele case added
1.6 June 2007 importance sampling now done within BEST part 2
outfile from part 1 formatted for use in BEST part 2
2.0 May 2008 Gene trees and Species trees estimated jointly in one MCMC
Uniform distribution for prior on species tree topology
population size estimates in output
2.1 July 2008 Users specify size of neighborhood aroung MT in proposal trees
Users specify cooling rate in annealing component.
2.2 October 2008 Routines optimized to improve speed
Increased upper limits on number of species and genes.
2.3 May 2009

August 2009
November 2009
January 2010
Summarizing trees in multiple allele case simplified
Bug fixed in output file formatting
Mac version optimized for type of processor (PowerPC vs Intel)
Bug fixed in parallel version
Beta version with GUI available

Please send reports of any bugs in this version or about general issues related to BEST to Liang Liu.

Questions regarding the Macintosh executable or compiling the source code for Macintosh computers (but not about BEST itself) should be sent to Liang Liu.

Questions about using the GUI should be sent to Dennis Pearl.