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MORGAN 2.5 replaced MORGAN 2.4.1 which superceded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.
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.
Unfortunately, owing to personnel retirements, the Lodscore programs cannot
yet be released under MORGAN 3. This beta-test version of MORGAN 3.0
includes the PedComp (kin, pedcheck), Genedrop (genedrop, ibddrop, markerdrop),
and Autozyg (lm_auto, lm_map, lm_ibdtests, lm_pval) programs only. However,
all subroutine libraries are included and working.
Also available:
| Name | Description | Size |
| MORGAN_V2.8.3 | tarred and gzipped | 1427kb |
| MORGAN_V3.0 (beta) | tarred and gzipped | 664kb |
MORGAN 2.8.3 contains updates, improvements and corrections over 2.8.2. The main changes consist of the removal of old LR-based MCMC lodscore programs (lm_lods and lm_schnell) to a new LR_Lods directory. Additionally program setup functions have been moved from Lodscore, Autozyg and LR_Lods directories to appropriate library directories. This facilitates the inclusion of a new program lm_twoqtl in the Lodscore directory: the new library TwoQTL is released in connection with this program. New gold standards for lm_multiple, including exact computation, and computation by component, are included in Lodscore/Gold. The gold standards for lm_twoqtl are also in this directory. Original gold standards for lm_auto (in Autozyg/Gold1) and lm_lods (in LR_lods/Gold1) have been reinstated with this release.
MORGAN 2.8.2 contains updates and improvements over 2.8.1. The main changes are in the lm_markers and new lm_multiple programs, with many changes relating to meiosis sampling and computation in the Sample subdirectory. Exact computation of lod scores on small pedigree components is implemented. Multiple-meiosis sampling is implemented, and used by lm_multiple. New gold standards have been added for exact computation and multiple-meiosis sampling. Old Gold1 gold standards for lm_lods and lm_auto are not released in this new version.
MORGAN 2.8.1 contains minor updates, corrections and improvements over 2.8.
Note there are no longer default allele frequencies for either trait loci or
markers.
With MORGAN 2.8 two new programs have been added to the Autozyg suite. These are Autozyg/lm_ibdtests by Saonli Basu and Autozyg/lm_map by William Stewart. Details of these programs may be found in the user documentation. Gold standards may be found in Autozyg/Gold2. Other changes consist only of minor fixes and updates to MORGAN 2.7.
With MORGAN 2.7, the MCMC main programs have been divided into IBD programs (Autozyg) and Lodscore programs. Two new programs are released (Lodscore/lm_schnell and Genedrop/markerdrop) and one replaced by a much more general program (Autozyg/lm_pval). A two-dimensional interactive graphics option has been added to Autozyg/lm_auto using OpenGL. More options and parameters added to the parameter file include an option for Kosambi map distances, and more general trait input and trait model specifications. Setup for many of the programs (especially those in Autozyg and Lodscore) has been unified, with new setup routines shared by all programs.
See the README_relnotes in the main MORGAN directory
for more information.
Also, MORGAN
users updating from previous MORGAN versions should read
Autozyg/README_IMPORTANT for changes in some parameter statements.
A brief history of MORGAN development.
(up to version 2.6)
Through version 2.8.1, MORGAN-2 was developed primarily by Myrna Jewett.
The tutorial is now fully updated for MORGAN 2.8.1 (August, 2007)
An updated examples file for use with MORGAN 2.8.3 is released April 2008.
If using the Tutorial with MORGAN 2.8.3, please be sure to download
the correct examples file. (See below: not the one linked within the
tutorial.)
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.
Also here are the simulated data used in
MORGAN 2.8.1 Tutorial and examples
Online version of the tutorial (paginated html)
An updated online version
available here.
This version of Aug 22, 2007, has updated final chaper on lm_map with new
example. The released download versions of tutorial and examples (August 11,
2007) have not been updated.
Examples files
A new, extended, and improved examples file is released August 2007.
All examples will run with MORGAN 2.8.1 (and also with 2.8.2, but there
will be some differences).
Name Description Date
Size
MORGAN 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
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.
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
ped_sims.tar.gz
Simulated data for program comparison
J. H. Rothstein
Dec 5, 2007
| UW - Statistics: Friday, 02-May-2008 15:07:25 PDT | Contact: Elizabeth Thompson <thompson@stat.washington.edu> |