IMa (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. IMa 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 IMa program and
for literature references please consult the
IM and IMa web page.
IMa can be run in M mode (run MCMC simulation to sample trees) or in L mode
(load and analyze trees sampled in previous runs). This interface also allows you to
combine the two modes, i.e., to run the L mode analysis immediately after an M mode run.
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 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
M mode followed by L mode
Upload your input file
For full description of all available
program options
refer to
IMaa
Documentation.
M mode command: (options -i and
-o may be omitted - they will be added automatically based on uploaded input files;
write in one line -
text will wrap around).
Please see this advice about the -L option.
L mode command: (options -i, -o,
and -r 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:
(
Show timeout info )
