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
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:
PANGAEA currently consists of ten packages:
Release history .
Currently active packages
MORGAN version 3
MORGAN version 2.9
(November 2008) remains available for those who wish to use it.
- MORGAN version 3.2:
Dec 2013; includes fully integrated and updated ibd_haplo and gl_lods programs
- MORGAN 3 Tutorial and examples for download.
contains some minor updates to the Dec 2012 release
Examples and tutorial text updated for MORGAN 3.1.1 (incl. IBD_Haplo), December 2012.
Original MORGAN-3 version October 2011; corrections and updates December 2011.
MORGAN SCRIPTS (July 2007),
SIMULATED TEST DATA (Dec 2007),
Linkage file examples (Dec 2009).
GIGI: Genotype Imputation Given Inheritance
- For other related scripts see also
SimSuite Ver 1.0 Scripts of the Wijsman group (released March 2009).
to translate from LINKAGE to MORGAN and examples; updated
for MORGAN 3.0.3, December 2011;
improved and re-released March 2012.
See the web page for this MORGAN-related package; version 1.04 released November 2013.
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 1.5 is released to CRAN, March 2013.
First release, March 2011. Version 1.2 released November 2011.
These R tools analyze the output of IBD_Haplo, producing various plots and
Documentation and tutorial included in the package tar file.
is now fully integrated into
MORGAN 3.1 (and later releases)
First release, October 2009. Release of version 2.1 October 2011.
The files to recreate the analyses of the January 2012 IBDmerge
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
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).
ALBERT (May 2006)
Eclipse (version 1.1);
Documentation (updated 10/2003)
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
For a brief release history, click