MORGAN 3.1.1 is released in November 2012:
The main changes are in major revisions and improvements of
use interface for ibd_haplo
in the IBD_Haplo program directory.
The gold standards, coding, and algorithms for this program are
significantly modified. The IBDgraph library has been added to the
released version of MORGAN: it is used by the beta test program gl_lods.
Other smaller changes are detailed in the README_relnotes file in MORGAN.
MORGAN 3.1 is released in April 2012:
The main change is the full integration of ibd_haplo as a MORGAN program
in the IBD_Haplo program directory,
with parameter statements and gold standards.
There has also been the continuing improvement of code and of gold standard
examples.
MORGAN 3.0.3 is released in October 2011:
There has been continuing code clean-up and improvement.
The combined program lm_linkage replaces
lm_multiple and lm_markers.
Both programs lm_twoqtl and civil remain
beta-test versions; the program gl_lods is also added as beta-test.
These progams are described in the MORGAN-3 Tutorial also released.
The IBD_Haplo directory (IBD_Haplo version 2.1)
is included in this MORGAN release; the ibd_haplo program and examples have
also been much cleaned up and improved.
MORGAN 3.0.2 is released in April 2011:
There has been extensive code clean-up and improvement to the Autozyg/gl_auto
and lm_auto programs.
lm_auto has been generalized to use the MCMC sampling options used also
by gl_auto, lm_multiple and lm_markers.
There is a new options to check marker data consistency in these MCMC programs.
Both programs lm_twoqtl and civil remain
beta-test versions.
The old LR_Lods programs lm_schnell and lm_lods, the IBD_Haplo programs,
and the Schnell development programs are NOT included
in this release.
The IBD_Haplo directory (IBD_Haplo version 2.0)
is available as a separate add-on.
MORGAN 3.0.1 is released in September 2010:
There has been extensive code clean-up and improvement to the new MORGAN 3.0
programs gl_auto and lm_twoqtl.
However, both programs lm_twoqtl and civil remain
beta-test versions.
The program lm_schnell and lm_lods of the LR_Lods program directory are
reinstated with this release.
The IBD_Haplo directory (IBD_Haplo version 2.0)
is also included within this
MORGAN release: it is also available as a
separate add-on.
Morgan 3.0 was released in November 2009:
with this version Morgan-3 was no longer beta-test!!
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.
The
online version of December 2012 (paginated html), corresponds to
the download version and examples files below.
This version replaces the version of Decmber 2011, with a new Chapter
for IBD_Haplo, and accompanying examples.
The text and examples for
other programs remain essentially unchanged.
| Name | Description | Date | Size |
| MORGAN 3.1.1 example files | Updated files for MORGAN 3.1.1 tarred and gzipped | December 2012 | 144 kb |
| Name | Description | Size |
| MORGAN-3 tutorial html version | Online paginated version: tarred and gzipped | 126kb |
| MORGAN-3 tutorial | Hyperlinked PDF | 748 kb |
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.
Note also if using Win32 executables, the runtime commands of the Tutorial examples and Gold standard examples may require slight modification.
| Name | Description | Size |
| MORGAN_V3.1.1; November 2012 | tarred and gzipped | 2804kb |
| 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
online version of September 2010 (paginated html), corresponds to
the download version and examples files below.
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.
Added December 2011: the basic script is updated for MORGAN 3.0.3 lm_linkage
program, and an example file for the binary trait added.
Also here are the simulated data used in
MORGAN 2.9 Tutorial and Examples
With the release of update online and download versions of the tutorial, with
fully updated Examples, in Sptember 2010, earlier versions of the Tutorial
and examples have been removed.
Online version of the tutorial (paginated html)
Examples files
See the tutorial for how to download and install your
Name Description Date
Size
MORGAN 2.9 example files Updated files for 2.9
tarred and gzipped September 2010
75 kb
Download versions of MORGAN 2.9 tutorial
Other versions (pdf, PostScript, etc.) are also available for download
(September 2010):
Name Description Size
MORGAN-tutorial html version
MORGAN-tutorial paginated html .
tarred and gzipped 446kb
222kb
MORGAN-tutorial info version gzipped
74kb
MORGAN-tutorial PostScript gzipped
287kb
MORGAN-tutorial hyperlinked PDF
.
598 kb
MORGAN-tutorial plain text version .
273kb
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
lnkg2lmlnk.tar.gz
From LINKAGE to MORGAN-3/lm_linkage
Hiep Nguyen and Ellen Wijsman
March 2012
example_m3_bin.tar.gz
Example output binary trait MORGAN-3 files
Elizabeth Thompson
December 2011
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: Wednesday, 26-Dec-12 | Contact: Elizabeth Thompson <thompson@stat.washington.edu> |