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.

References:

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

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.

You will need to upload your data file and a control file which contains the parameters you want to run. Please refer to the MCMCcoal documention or the MCMCcoal web page for more information on the format of these files.

Please note that if you are using an absolute path to an input file in your control file, it will not be recognized on our system. If the first line of your control file contains an absolute path to your data file, it will be modified to just the name of the data file.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

Please acknowledge us in all publications and presentation of work that used our resources using the following text.

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