Segtools

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.
After installing Bioconda, install Segtools with:
Segtools requires the following prerequisites:
Once these prerequisites are properly installed, install Segtools with:
To upgrade an existing Segtools installation to the latest version, type the following command at the shell prompt:
* We have only tested this software on the following platforms. We would love to extend our support to other systems in the future, and we would gladly accept any contributions toward this end.
As a last resort, or for situation in which you want to try Segtools without dealing with the hassles of heterogeneous system configurations, we have created a VirtualBox Virtual Machine, loaded with Segtools, some sample data, and all necessary prerequisites.
Warning, this is a large (551 MB) file: VM for Segtools 1.1.6
The application's documentation is available in three formats:
To stay informed of new releases and other important information, please subscribe to the segtools-announce mailing list.
There is also a segtools-users mailing list for general discussion and questions about the use of Segtools.
If you want to report a bug or request a feature, please do so using the Segtools issue tracker.