Version 1.2, March 2008

**Notes added by Ziheng on 20 May 2010: The
Bayesian program MCMCcoal (together with the simulation program
MCcoal) is replaced by the new program BP&P (Yang and Rannala 2010).
The likelihood program Ne3sML is replaced by the program 3s (Yang
2010). If you need to use the new methods described in those two 2010
papers, please use the newer programs instead. **

**MCMCcoal** is an ANSI C program that implements the Bayesian Markov
chain Monte Carlo (MCMC) algorithm of Rannala & Yang (2003) for
estimating species divergence times and population sizes from DNA
sequence alignments at multiple loci. Consult the paper for details
of the model assumptions and the theory. The program can also be
used to analyze a sample of sequences from one modern species under
the standard neutral coalescent to estimate theta.

Download MCMCcoal1.2a.tar.gz, which contains win32 executables as well as C source code for compiling on unix/linux/OSX. Make sure you save the file as MCMCcoal1.2a.tar.gz.

Version 1.2a (October 2010): The program occasionally hangs during the MCMC, when the proposal is reflected infinitely. This is now fixed. Anyway try to use bpp instead as I won't be updating this program.Version 1.2 (March 2008). The following changes were introduced relative to version 1.1: addition of two models of mutation rate variation among loci: one using fixed locus rates estimated externally, and another of random variable rates across loci; two options for locus-specific heredity multipliers (inheritance scalars); a change of parametrization concerning species divergence times; and a model of random sequencing errors. See the documentation (MCMCcoalDOC.1.2.pdf) for details. Those changes were introduced in Burgess & Yang (2008).

**Ne3sML**. The win32 program Ne3sML
program implements the ML method of Yang (2002). The program uses
numerical integration routines in Mathematica so you have to have
Mathematica 3.0 or later to run the program. Download the archive Ne3sML.win32.v1.1.tar.gz. Make
sure you save the file as Ne3sML.win32.v1.1.tar.gz. The archive
includes ANSI C source codes and the Mathematica package, as well as a
readme file. To compile for MAC OSX or UNIX, you probably need to
look at my notes for windows and also the documentation about mathlink
AddOn supplied by Wolfram.

References

Burgess, R. and Z. Yang (2008). Estimation of hominoid ancestral
population sizes under Bayesian coalescent models incorporating
mutation rate variation and sequencing errors.
*Mol. Biol. Evol.* 25: 1979-1994.

Rannala, B. and Z. Yang (2003). Bayes estimation of species
divergence times and ancestral population sizes using DNA sequences
from multiple loci. *Genetics* 164: 1645-1656.

Yang, Z. (2002). Likelihood and Bayes estimation of ancestral
population sizes in Hominoids using data from multiple loci. *Genetics*
162: 1811-1823.

Yang, Z. (2010). A likelihood ratio test of speciation with
gene flow using genomic sequence data. *Genom. Biol. Evol.* 2:200-211.

Yang, Z., and B. Rannala. (2010). Bayesian species delimitation using
multilocus sequence data. *Proc. Natl. Acad. Sci. U.S.A.* 107:9264-9269.

Last modified: May 2010