GOTO NEW VERSION!) Version is 3.6  [Fall 2013]

Updated prior system, including a gamma distribution prior. Addition of prior information into the histograms of the PDF outfile.  MacOS 106, 10.7, and 10.8 version now have an experimental installer. I switched the copyright license to the MIT opensource license.

Important additional information to help run recent version of migrate:

  1. Most recent paper on migrate technology: Beerli and Palczewski 2010: Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations. Genetics (2010) vol. 185 pp. 313--326 (LINK)

  2. Tutorial on how to compare population genetic models (LINK)

  3. Opinion about issues with divergence and accuracy of migration rates (LINK)

Known problems with current version:

  1. no known problem (yet)


estimation of population sizes

and gene flow using the coalescent

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes.
Migrate uses Bayesian inference (or maximum likelihood) to jointly estimate all parameters. The analysis can be constrained to subsets of migration patterns, such as setting some migration rates between populations to zero or constrain to symmetric rates or average over all migration rates, or use Bayes factors to compare different hypotheses. Migrate can use single-locus or multi-locus data: sequence data using Felsenstein's 84 model with or without site rate variation, single nucleotide polymorphism data, microsatellite data using a stepwise mutation model or a brownian motion mutation model, and electrophoretic data using an 'k+1' allele model.
The output comes in two flavors: PDF and TEXT file. The file can contain:  
Bayesian inference: Estimates of maximum posterior values of parameters and credibility intervals in table form, figures of posterior distribution of parameters. Indications of convergence and effective sample size, presentation of frequency of migration events over time, very approximate skyline plots, genealogy with best likelihood (Printable through ET (eventtree -- or after some editing in Figtree (Andrew Rambaut), calculation of marginal likelihood that can be used to compare different models. 
Maximum likelihood: Estimates of all migration rates and all population sizes, assuming constant mutation rates among loci or a gamma distributed mutation rate among loci. Profile likelihood tables, Percentiles, Likelihood-ratio tests, and simple plots of the log-likelihood surfaces for all populations and all loci. (not all plots are implemented in the PDF, yet). Genealogy with best likelihood. 





Research is and was supported by grants of the National Institutes of Health (R01 GM078985, 2006-2011 -- NSF/NIGMS Mathematical Biology program) and the National Science Foundation (DEB-0822626, 2008-2013 and  DEB-1145999, 2012-2014)