The genomic association tester (GAT) tests for association between intervals in a genome analysis context.
GAT answers the question, if a set of intervals on a genome is statistically significantly associated with one or more other sets of genomic intervals. Assocation typically means overlap, but also other measures like the distance between elements can be tested.
The tests are performed by simulation and within a genomic context. The simulation part takes care of segment length distribution. The genomic context takes into account chromosomal location and optionally isochores.
The software is available for download on pypi:
pip install gat
Please see http://gat.readthedocs.org/en/latest/ for a manual and tutorials.
A GAT user group is at:
https://groups.google.com/forum/?fromgroups#!forum/gat-user-group
The latest release can be downloaded from pypi at https://pypi.python.org/pypi/gat