A toolset for working with human genetic variation data

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.

Latest Release

The latest PLINK/SEQ release is 0.08 (released 22 March 2012). It is available on the download page. This contains a large number of new features, bug fixes and improvements, described here; we also maintain a list of known issues. Any users of version 0.07 or prior are strongly advised to upgrade.

A beta version of version 0.09 is also available from the Bitbucket repository; this will replace 0.08 as the official, stable release very soon.

Getting Started


PLINK/SEQ users are welcome to participate in the Google Group. Support questions should be posted there.