With this version (November 2009), we are no longer beta-test!!
MORGAN-3 is ready for full use, although 2.9 remains available for those
who wish to use it.
Under MORGAN 3.0 traits are separated from trait loci (tlocs) permitting genotypes at several tlocs to influence a trait or genotypes at a tloc to influence several traits.
In addition to the programs Autozyg/gl_auto and PedComp/translink of the second (March 2009) beta-test release, we have a new program Lodscore/civil. The two Lodscore programs civil and lm_twoqtl remain to be fully tested. All other programs are ready to go!!
The old programs LR_Lods/lm_lods and LR_Lods/lm_schnell, and the real-time graphics display library GLDisp are not available under MORGAN 3.0.
In December 2009, IBD_Haplo: an add-on for MORGAN 3 is released.
See also MORGAN NEW DEVELOPMENTS for information on new capabilities in MORGAN 2.8.2 and 2.8.3, and uncoming MORGAN developments: this information also pertains to MORGAN 2.9.
And see MORGAN 2.9 Executables for download of Max OSX and Win 32 executables.
| Name | Description | Size |
| MORGAN_V3.0; 11/09 | tarred and gzipped | 1513kb |
| MORGAN_V2.9 (with 11/08 bug fix) | tarred and gzipped | 1393kb |
| MORGAN_V2.9 Win32 executables | zip archive | 6527kb |
| MORGAN_V2.9 Max OSX Binary | zip archive | 7343kb |
With this version (November 2009) of MORGAN 3.0, we are no longer beta-test!!
MORGAN-3 is ready for full use.
Under MORGAN 3.0 traits are separated from trait loci (tlocs) permitting
genotypes at several tlocs
to influence a trait or genotypes at a tloc to influence several traits.
In addition to the programs Autozyg/gl_auto and PedComp/translink of the second (March 2009) beta-test release, we have a new program Lodscore/civil. The two Lodscore programs civil and lm_twoqtl remain to be fully tested. All other programs are ready to go!!
The old programs LR_Lods/lm_lods and LR_Lods/lm_schnell, and the real-time graphics display library GLDisp are not available under MORGAN 3.0.
A full working version of the MORGAN-3 package was released March 2009, including two new programs Autozyg/gl_auto and PedComp/translink, but much testing and documentation remained to be done.
The first (March 2008) beta-test version of MORGAN 3.0 was only a partial package: it did not contain the PolyEM, and Lodscore programs.
The main change in MORGAN 2.9 consists of a complete code overhaul
to meet c89 standards, and testing on multiple platforms. This resulted
in numerous bug fixes. Additionally there have been improvements in
multiple meiosis sampling and exact computation algorithms. Despite this
some known problems on some operating systems exist: see README_bugs_v2.9
in the main MORGAN directory of the release. (An lm_multiple bug is now
fixed, Nov 2008.)
Thanks to Dr. Michael Na Li, University of Minnesota, we also release
Mac OSX and Win32 Windows executables.
The Win32 version was compiled under Vista, and also tested with WinXP.
The Mac version is Universal Binary and works on both Intel and PPC G4/G5
based Macs. It has been tested only under Mac OS 10.5 Leopard.
Apart from bug fixes, MORGAN 2.9
is expected to be the final MORGAN-2 release. Future development will be
under MORGAN-3.
See the README_relnotes in the main MORGAN directory
for more information.
Users converting from MORGAN-2 to MORGAN-3, please consult the
README_userdoc files and README_convert2_3.0 in the program directories,
and see also the examples in the Gold subdirectories.
MORGAN-2 users updating from previous MORGAN-2 versions should read Autozyg/README_IMPORTANT for changes in some parameter statements.
A brief history of MORGAN development.
Through version 2.8.1, MORGAN-2 was developed primarily by Myrna Jewett.
With version 2.9, and continuing development of MORGAN 3.0 (initiated by
Myrna Jewett), Steven Lewis takes over.
The released download versions of tutorial and examples (August 11,
2007) for MORGAN 2.8.1 have not yet been updated.
The
updated online version of the MORGAN 2.8.1 tutorial
is the version of July 23, 2008.
It has updated final chaper on lm_map with new
example (August 22, 2007) and miscellaneous other corrections.
Released December 2009, we have also a
test version of the new
online tutorial for MORGAN 2.9 (December 2009).
After testing, a full release of this version of the tutorial will
replace all earlier versions.
An updated examples file for use with MORGAN 2.8.3
is released April 2008.
If using the Tutorial with MORGAN 2.8.3 or later, please be sure to download
the correct examples file. (See below: not the one linked within the
tutorial.)
An updated tutorial for MORGAN 2.9 is is process of release. This
version links to the
MORGAN 2.9 example files
See the tutorial for how to download and install your
We propose to provide useful scripts for translation of data files from
(for example) LINKAGE format to MORGAN format. These were mainly developed
for in-house purposes. They have been checked and are documented, but are
provided with no guarantee. Download, unzip and untar, and use freely
(with Acknowledgement). Documentation is included in the tar file.
Added 2009 are two example Linkage files that work with these scripts,
one for a binary trait and the other for a quantitative trait.
Also here are the simulated data used in
MORGAN 2.8 and 2.9 Tutorial and examples
Online version of the tutorial (paginated html)
Examples files
A new, extended, and improved examples file is released August 2007.
All examples run with MORGAN 2.8.1 (and also with 2.8.2, but there
are be some differences).
Name Description Date
Size
MORGAN 2.8.1 example files files for 2.8.1, 2.8.2
tarred and gzipped August 2007
106kb
MORGAN 2.8.3 example files files for 2.8.3
tarred and gzipped April 2008
116kb
MORGAN 2.9 example files new files for 2.9
tarred and gzipped December 2009
97kb
Download versions of tutorial
Other versions (pdf, PostScript, etc.) and the directory of test
example files are available for download.
These are now for the released version of August 2007.
New MORGAN 2.9 tutorial will be released after testing.
Name Description Size
MORGAN-tutorial html version
MORGAN-tutorial paginated html .
tarred and gzipped 373kb
102kb
MORGAN-tutorial info version gzipped
63kb
MORGAN-tutorial PostScript gzipped
260kb
MORGAN-tutorial hyperlinked PDF
.
568 kb
MORGAN-tutorial plain text version .
187kb
MORGAN file translation scripts and Test Data
Multipoint linkage analysis with many multiallelic or dense diallelic
markers: Markov chain Monte Carlo provides practical approaches for genome
scans on general pedigrees
Ellen M. Wijsman, Joseph H. Rothstein, and Elizabeth A. Thompson
American Journal of Human Genetics, 79: 846--858 (Nov 2006)
Name Description Author
Date
lnkg2lmm.tar.gz
From LINKAGE to MORGAN/lm_markers
J. H. Rothstein
July 25, 2007
example_bin.tar
Example binary trait Linkage files
J. H. Rothstein and E. M. Wijsman
November 2009
example_quant.tar
Example quantitative trait Linkage files
J. H. Rothstein and E. M. Wijsman
November 2009
ped_sims.tar.gz
Simulated data for program comparison
J. H. Rothstein
Dec 5, 2007
| UW - Statistics: Saturday, 26-Dec-2009 23:09:58 PST | Contact: Elizabeth Thompson <thompson@stat.washington.edu> |