LAMARC is a program for doing Likelihood Analysis
with Metropolis Algorithm using Random Coalescence. Lamarc
estimates effective population sizes, population exponential growth rates, a
recombination rate, and past migration rates for one to n populations
assuming a migration matrix model with asymmetric migration rates and different subpopulation
sizes. This version can use DNA or RNA sequence data, SNPs, microsatellites, or electrophoretic
data. The program can produce: estimates of recombination rate, migration rates between each
population pair, population sizes (assuming constant mutation rates among loci), population
exponential growth rates, profile likelihood tables, and percentiles.
You will need to upload your data file in the proper (*.xml) format containing
the parameters of the run. You can also upload an optional summary file. Make sure that your
input file 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.
The best way to obtain the data file is to have the LAMARC file converter
lam_conv.exe
installed on your
local machine and run it from the command line so that all the parameters of the run can be set
up using the program's menu. Then upload the data file and the tar archive if there are additional input files to the
CBSU cluster using this web page and submit the job. For more information on running LAMARC
and the file converter, please consult the
LAMARC web page.
It is generally a good idea to actually try to run
LAMARC on your local
machine with your particular data files before submitting the job to the cluster. This will
allow you to catch and fix any mistakes you may have in your input files.
If you get as far as starting the "Initial Chain", it should run successfully here.
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.
Job name:
(will be set to the name of input file)
Upload your data file
Upload your Summary File (Optional)
Cluster:
This application can't run at this time - no suitable clusters
or you are not authorized to use the service.
The service is available only to Cornell students, faculty, and staff.
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