IMa

Category

Bioinformatics

Program On

pcluster

Version

May 06, 2009

Author / Distributor

Jody Hey, Rutgers University (see http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM)

Description

IMa is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. It uses a method that provides estimates of the joint posterior probability density of the model parameters. IMa also allows log likelihood ratio tests of nested demographic models. IMa is based on a method described in Hey and Nielsen (2007 PNAS 104:2785/2790).

Running Program

To run IMa interactively, invoke the application with ima followed by the options you want to use.

For example:

 ima -i mydata -o mydata.out -q1 10 -m1 10 -m2 10 -t 10 -b 1000 -L100 -s123 -p45

If you are planning to run IMa interactively for more than 10 minutes, please run it on an interactive node instead of the pcluster headnode.

IMa can also be run on the batch queue, which is recommended if you are planning to run long jobs. Here is an example of how this can be done:

First create a script file with the IMa command line.

Sample script file sub.sh to run IMa using input parameters from a file called mydata and it saves the output of the execution in a file called mydata.out: Please replace your_working_directory by the path to the directory in which you are working. For example, if you are working in a directory called test under your home directory, use ${HOME}/test in place of your_working_directory

 #!/bin/csh
 cd your_working_directory
 ima -i mydata -o mydata.out -q1 10 -m1 10 -m2 10 -t 10 -b 1000 -L100 -s123 -p45

Then submit the script file sub.sh to the queue:

ugsub T1-i1-t1-24h sub.sh

The queuename T1-i1-t1-24h used in this example can be replaced by other one processor queuenames (that is, the maximum runtime of 24h can be changed). Please refer to Running Jobs on pcluster for more information on how to submit batch jobs on pcluster.

Documentation

IMa user guide is available in /usr/local/IMa/manual/

Some relevant papers are available in /usr/local/IMa/papers/

Installation

Installed in /usr/local/IMa and the executable is in /usr/local/bin, a directory that is on user's default path.

System

64-bit Linux