What’s new in EIGENSOFT

Enhancements to this version include keeping track of reference/variant alleles in all file formats, handling data sets up to 8 billion genotypes, and functionality to output SNP weightings of each principal component.

Thorough tests of this software are ongoing. Changes to this beta release based on our tests or your comments will be posted at this web site. Users preferring to use thoroughly tested code may instead wish to use EIGENSOFT version 1.01, available at the Reich lab software page.

10/10/07: Fixed bug in translation from .pca.evec file to .pca file when running smartpca.perl (previous versions of EIGENSOFT are not affected).

11/21/07: Fixed bug in twstats (previous versions of EIGENSOFT are not affected). Added new documentation on producing large files in EIGENSTRAT format. Added new documentation on running on QTL data.

12/30/07: Fixed bug leading to inappropriate error message in some large data sets. Added to documentation for running on large data sets.

01/03/08: Fixed bug related to 12/30/07 changes.

We strongly encourage users to register before downloading the software.