PANGAEA
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
(eathomp@u.washington.edu).
IMPORTANT NOTICE: JANUARY 2006 From 2006, all MORGAN source code is made
freely available for any use, including modification and redistribution:
PANGAEA: See the
Release history , for the full list of software
described below.
Below see
MORGAN
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).
- For other related scripts see also
SimSuite Ver 1.0 Scripts of the Wijsman group (released March 2009).
- Script
to translate from LINKAGE to MORGAN and examples; updated
for MORGAN 3.0.3, December 2011;
improved and re-released March 2012.
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.
RELATED SOFTWARE
See
Dr. Wijsman's softare distrbution page for
- GIGI: Genotype Imputation Given Inheritance
version 1.05 released Aug 16, 2014.
- GIGI-pick: Using GIGI to select subjests for sequencing.
Released Feb 7, 2014.
- GIGI-check: Using GIGI to detect Mendelian-consistent errors.
Released Apr 25, 2014.
- famSKAT-RC and Ped_Pop: Combining genotype impuation from GIGI and BEAGLE.
Released, July 25, 2014.
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).
OTHER PACKAGES
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.