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.

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.

Online version of the tutorial (paginated html)

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.