MORGAN

Use of software agreement:PLEASE READ

See also: Release history

Now available:

MORGAN 3.2 and MORGAN V2.9


MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis,
developed under PHS grant GM-46255, Genetic Epidemiology of Complex Traits .

MORGAN 3.2: The new MORGAN framework
and MORGAN-3 Tutorial and examples

MORGAN V2.9 and MORGAN 3.2

Name Description Size
MORGAN_V3.2; December 2013 tarred and gzipped 2808kb
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

MORGAN 3.2 is released in December 2013:
There are major developments of both the programs gl_lods and ibd_haplo. The gl_lods program is no longer beta-test. Its input is developed, no longer requiring dummy pedigree amd marker information, and it can handle multiple components. ibd_haplo also has significant improvements in the output options, and in the approximations used in the transition state matrix. More minor changes have been made to other programs. For example, output options for gl_auto are improved. In all MCMC-based programs, pedigree components with no informative meioses (e.g. a parent-offspring trio) are now cleanly dealt with, and bypassed in computation. For additional details see the README_relnotes file in MORGAN.

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.


MORGAN 3.1.1 Tutorial and Examples

Online version of the tutorial (paginated html)

The online version of July 2013 (paginated html) contains some minor updates
relative to the released December 2012 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.

Examples files

See the tutorial for how to download and install your
Name Description Date Size
MORGAN 3.1.1 example files Updated files for MORGAN 3.1.1
tarred and gzipped
December 2012 144 kb

Download versions of MORGAN 3.1.1 tutorial

Hyperlinked pdf, and paginated html versions are also available for download (December 2012)
Name Description Size
MORGAN-3 tutorial html version Online paginated version:
tarred and gzipped
126kb
MORGAN-3 tutorial Hyperlinked PDF 748 kb

MORGAN 2.9: The old MORGAN framework

MORGAN 2.9 is a code clean-up and multiplatform tested version: known problems in 2.8.3 are fixed. An additional bug (affecting only lm_multiple) is fixed in November 2008 release.
MORGAN 2.8.3 contains updates and improvements over 2.8.2, including a beta-test version of the new lm_twoqtl program.
MORGAN 2.8.2 contains updates and improvements over 2.8.1, including a new multiple-meiosis MCMC sampler.
MORGAN 2.8.1 contains minor updates, corrections and improvements over 2.8.
MORGAN 2.8 replaces MORGAN 2.7, containing two additional programs.
MORGAN 2.7 replaces MORGAN 2.6 and MORGAN 2.5, for Unix/linux operating systems.
MORGAN 2.5 replaced MORGAN 2.4.1 which superceded both MORGAN 2.4 and MORGAN 2.3.2
MORGAN_V2.3.x supercedes both MORGAN V2.2 and MORGAN V1.1.2

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.

MORGAN 2.9 Tutorial

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.

Note also if using Win32 executables, the runtime commands of the Tutorial examples and Gold standard examples may require slight modification.

Also available (New 2007):

MORGAN Scripts: Scripts for translating files to Morgan input format.
and Test data: for comparison of programs.




Morgan-2 is history!! New users, try MORGAN-3

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.

A brief update on last updates to MORGAN-2

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.

Release history

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.




MORGAN under Windows: WHY???

MORGAN may be (in principle) installed under Windows: executables should then be placed in the directory in which programs are to be run. See the documentation and tutorial for more information. We cannot currently answer any questions regarding Windows installation. Instead, we recommend the use of a linux-system emulator such as Cygwin.



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)

The online version of September 2010 (paginated html), corresponds to the download version and examples files below.

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


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
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, 04-Dec-13 Contact: Elizabeth Thompson <eathomp@u.washington.edu>