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4th February 2016
We are aware that the version of PowerMarker available from this site is nonfunctional, giving a message that it has expired. We are trying to find a copy of the original source code to recompile PowerMarker, but we are not very hopeful about that. Even though it remains widely used, we have not supported or updated PowerMarker for over 10 years. At this point the only way to run the software is by changing your computer.s calendar date. Please watch the web site for a message announcing either a revised download or the end of PowerMarker.

What's new?
  • Version 3.25 released on 2/5/2006. This is a permanent version!! Please cite the Bioinformatics paper. Choose 'How To Cite' from Help menu to see more details.
  • Version 3.09 released on 7/14/2004. Support 120 dpi settings.
  • Version 3.08 released on 6/14/2004. Fixed a bug in core set selection.
  • Version 3.07 released on 3/20/2004. (1) New SNP identification tool (2) Fix several minor bugs.
  • Version 3.03 is available for download. (1) Fix a bug in batch export. (2) New functionality for single haplotype phase assignment. (3) Allow for all-missing individuals for most analyses.
  • PowerMarker V3.0 was officially released on January 30th, 2004. Full documentation is included.
  • The following functions are disabled in PowerMarker: (1) Marker selection for haplotype data, genotype data and trio data (2) Population structure inference based on EM algorithm (3) Logistic regression and least angle regression for association study. The author is stilling working on the publications. The algorithms have been implemented and tested with simulated data. Please contact the author if you are interested in these algorithms.
What's PowerMarker?

PowerMarker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. See analysis to check out the versatility of PowerMarker. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results. Download PowerMarker now and speed up your data analysis!

Top ten features in PowerMarker
Unique analyses Implements population specific F-statistics, CoreSet analysis, structure inference based on EM, trio haplotype estimation, robust marker selection. Not available in any other package.
GUI-based batch system Support multiple dataset. Multiple threading system will allow the user to cancel or pause/resume the analysis anytime. Results will be automatically saved.
2D Viewer Support user-defined plotting. Support series of different levels of significance. Plot can be exported as image or graphic.
Excel integration Integrate with Excel. Table-like data objects can be directly opened in Excel. Easily import tables from Excel to PowerMarker. Directly call Excel for triangle plot.
Object explorer Manage all the data objects in an object explorer. Support drag and drop, allow the user to create new folders.
Haplotype estimation Estimate haplotype frequency using EM/Bisection EM algorithm. Up to 100 times faster than any other implementations.
Frequency-based distance Support 19 different distances for frequency data.
Disequilibrium analysis Include Hardy-Weinberg test/statistics, two-locus linkage disequilibrium test/statistics/2D matrix, multi-locus linkage disequilibrium test.
Batch import/export Import dataset from a few clicks! Support batch import for advanced users. Export all the data objects in a project to text files or tables!
SNP simulation Implement a coalescence model with or without recombination hotspots
PowerMarker's graphic user interface

The graphic interface allows the user to

  • Perform 30+ different analyses
  • Manage projects and a variety of data objects
  • Import data from raw formats
  • Export data to other formats
  • Sample/partition data objects
  • Convert data objects
  • View all the data objects
  • Generate CoreSet scripts
  • 2D plotting, triangle-plotting
  • Open data objects in Excel/TreeView/Image editor

Jack Liu  2004
Email: powermarker@hotmail.com