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Pedigree Analysis for Genetics

(and Epidemiological Attributes)

IMPORTANT NOTICE: MARCH 2005 Consequent on UW's decision to cease Anonymous FTP support, all download links have been moved to a web-based source.
If you have problems with any download links, please try this link, and also report problem to Elizabeth Thompson (

IMPORTANT NOTICE: JANUARY 2006 From 2006, all MORGAN source code is made freely available for any use, including modification and redistribution:

Use of software: PLEASE READ

PANGAEA: See the Release history , for the full list of software described below.

Below see



  • MORGAN version 3.4
  • MORGAN version 2.9 (November 2008) remains available for those who wish to use it.
  • MORGAN SCRIPTS (July 2007), SIMULATED TEST DATA (Dec 2007), and Linkage file examples (Dec 2009).

    IBD Packages

  • IBD_Stitch: updated July 2016.
    Chris Glazner's Haskell code (Latest release, June 25, 2014), is available from github: see the page for information.
    The page is updated July 2016, with added installation and tutorial instructions, and examples zip file added August 2016.
  • SMARTree Mathematica code by Chaozhi Zheng for the analyses of MCMC
    inference of local coalescent trees described in Zheng et. al. (2014; Journal of Molecular Evolution).
    Released May 2014. Or, for a more recent option, try this github link.
  • JointIBD Mathematica code by Chaozhi Zheng for the analyses of MCMC
    inference of IBD states described in Zheng et. al. (2014; Journal of Computational Biology).
    Released February 2014.
  • IBD_Create Version 2.0 Programs to generate IBD at varying LD
    New release with significant updates and reorganization of programs.
    See the documentation for details. Version 1.0 released October 2011.
  • IBDhaploRtools Version 1.7 is released to CRAN, July 2014.
    First release, March 2011. Version 1.2 released November 2011.
    These R tools analyze the output of IBD_Haplo, producing various plots and summary statistics.
    Documentation and tutorial included in the package tar file.
    Version 1.5 (due to Fiona Grimson) was released to CRAN, March 2013
    The current release is version 1.7, July 2014.
  • IBD_Haplo is now fully integrated into MORGAN 3.1 (and later releases)
    First release, October 2009. Release of version 2.1 October 2011.


  • See Dr. Wijsman's softare distrbution page for

  • The files to recreate the analyses of the January 2012 IBDmerge paper: Glazner, C. G., and Thompson, E. A. (2012).

  • IBDgraph 2.0: another C-library add-on for MORGAN 3 with brief install and test run documentation for python and C.
    First upload, March 2010; Version 2.0.1 released August 2010.
    For a description of this software see Koepke, H.A., and Thompson, E. A. (UW Statistics Technical Report #567).


    Maintained packages

    Old packages

    This collection of packages and documentation is managed by Dr. Elizabeth Thompson

    The development of packages MORGAN (2 and 3), the IBD packages, Loki (up to 2.1.2), Eclipse and InSegT were supported by NIH Grant GM-46255. Other packages were supported by other research funds.

    For specification in the format of the Rockefeller list of genetic analysis software, click here.

    For a brief release history, click here.

    UW - Statistics: Saturday, 07-Sep-19 Contact: Elizabeth Thompson <>