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
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.
(will be set to the name of data file)
(will be set after data file is selected)
Upload your data file
Upload your parmfile
Upload optional input files
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