Release History

  • October 8, 2013 : Release version 1.2
Bug corrections:
  • November 15 : regression from version 1.1 corrected (kfrq files), please update to new version.
  • Optimize cluster frequencies calculations to handle very large datasets
New features:
  • Added the --no-kfrq option to avoid writing down cluster frequencies to disk (useful for large datasets where these files can grow very large).
  • Distribution of a source package to install hapflk on systems not covered by binary executables
  • June 13, 2013 : Release version 1.1

As bugs were identified in the 1.0 version, all users should upgrade to 1.1.

Bug corrections:
  • The kinship matrix estimation routine had a bug leading to an under-estimation of internal branch lengths of the population tree. Population fixation indices (diagonal of the F matrix) were not affected.
  • When Individuals with the same name are found in the input files a warning is issued.
  • Numerical instabilities were encountered when estimating the fastPHASE model
New features:
  • The outgroup population can now be kept for the analysis with the new --keep-outgroup flag.
  • February 15, 2013 : Release version 1.0
Notes : a lot of code rewriting, option names are not compatible with Initial release.
New in this version:
  • Support for phased / inbred lines datasets
  • Support for plink binary files
  • October 26, 2012 : Initial Release v1-alpha