Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Oct 2011.
Exploratory analysis of genomic segmentations with Segtools.
BMC Bioinformatics, 12:415; doi:10.1186/1471-2105-12-415

Segtools is a Python package for analyzing genomic segmentations. The software efficiently calculates a variety of summary statistics and produces corresponding publication quality visualizations. The overall goal of Segtools is to provide a bird's-eye view of complex genomic data sets, allowing researchers to easily generate and confirm hypotheses.

Segmentations should be in BED4+ or GFF format, with the 'name' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.