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PLINK 1.9 vs PLINK 2.0: catalog facts
PLINK 1.9	PLINK 2.0
Best for: Researchers analyzing genome-wide association and genetic variation data	Best for: Researchers working with large genetic datasets and association analyses
Free Free and open source under GPL-3.0-or-later.	Free Free and open source under the GPL-3.0-or-later and LGPL-3.0-or-later licenses.
Windows, macOS, Linux, Command line	Windows, macOS, Linux, Command line
Handles several common genetic data formats Includes association, linkage disequilibrium, and population analyses All 3 strengths for PLINK 1.9 Handles several common genetic data formats Includes association, linkage disequilibrium, and population analyses Provides binaries for Linux, macOS, and Windows	Supports multiple genetic data formats Includes data management, statistics and association analysis All 3 strengths for PLINK 2.0 Supports multiple genetic data formats Includes data management, statistics and association analysis Provides builds for Linux, macOS and Windows
Some PLINK 1.07 operations are unsupported or obsolete Command-line interface requires familiarity with genetic data workflows	Documentation identifies the software as a beta
Downloadable app	Downloadable app
Open source	Open source
License: GPL-3.0-or-later	License: GPL-3.0-or-later and LGPL-3.0-or-later
Not stated if an account is needed	Not stated if an account is needed
Not stated if it works offline	Not stated if it works offline
Official website Full listing and sources Sources for PLINK 1.9 cog-genomics.org/plink/1.9 Catalog checked October 8, 2026	Official website Full listing and sources Sources for PLINK 2.0 cog-genomics.org/plink/2.0 Catalog checked October 8, 2026

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