IMa2 (by J. Hey and R. Nielsen) is an
implementation of the MCMC method for the analysis of genetic data under the
Isolation with Migration model of population divergence. IMa2 applies this model
to genetic data drawn from a pair of closely related populations or species.
The results are estimates of the marginal posterior probability densities for
each of the model parameters. For detailed description of the IMa2 program and
for literature references please consult the
IMa2 web page.
The only major conceptual addition to IMa2 that makes it different from the original
IMa program is that it can handle data from multiple populations. This requires that the user specify a
phylogenetic tree. Importantly the tree must be rooted and the sequence in time of internal nodes must be
known and specified.
The program model for IMa2 can accept a
large number of parameters. It should not be used with large models without a large
amount of data. However, if you are using a large amount of data, the program will
take a very long time to run.
IMa2 can be run in M mode (run MCMC simulation to sample trees) or in L mode
(load and analyze trees sampled in previous runs).
To select the desired mode of operation - pick the corresponding Run type button.
You will have to upload the main input file, and, if running in L mode, also the
tree file generated in a previous M mode run. You will also need to supply the
command line options for one or both operating modes, depending on the Run type chosen.
Note that the L mode command line must be consistent with the M mode command
used to generated the tree sample. The formats of the input file and command lines are described in
the IMa2 documentation. New users
should first read published papers and the
Introduction
to IM and IMa Documentation.
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)
Output file:
(will be set after input file is selected)
Run type
M mode
L mode
Upload your input file
Upload parameter prior file (required with option -g)
Upload saved Markov chain state file (required with option -f)
For full description of all available
program options
refer to
IMa2a
Documentation.
M mode command: (options -i, -f, -g and
-o may be omitted - they will be added automatically based on uploaded input files;
write in one line -
text will wrap around).
L mode command: (options -i, -o, -f, -g, -v
and -w may be omitted - they will be added automatically based on uploaded input
and tree files; the L mode command must be consistent with the M mode
command used to generate the tree files; write in one line -
text will wrap around).
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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