MIGRATE is part of series of programs in the package Lamarc. It estimates effective population sizes and past migration rates between n populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. MIGRATE uses maximum likelihood or Bayesian inference to jointly estimate all parameters. It can use sequence data, single nucleotide polymorphism data, microsatellite data using a stepwise mutation model or a brownian motion mutation model, and electrophoretic data using an 'infinite' allele model. The output can contain: 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. For detailed description and for literature references please consult the web page.

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.

You will need to upload your data file in the proper format and the parmfile containing the parameters of the run. In some cases, besides data file you will also need other optional input files, which have to be uploaded as a tar archive. Make sure that parmfile properly references the names of all the input files, and that no absolute path names (i.e., the ones containing strings like "C:\") are given. Also, make sure that the parameter menu is set to "NO" in parmfile.

During the run you will be able to monitor the standard output from the program using a link provided in a notification e-mail. All the output files will be available through ftp in a form of a gzipped tarball (a tgz file), updated every hour and accessible through a link in a notification e-mail.

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