MORGAN HISTORY

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MORGAN 2.5 replaced MORGAN 2.4.1 which superceded both MORGAN 2.4 and MORGAN 2.3.2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

Some MORGAN 2.x history

Apart from bug fixes, MORGAN 2.9 is expected to be the final MORGAN-2 release. Future development will be under MORGAN-3.

For more details of MORGAN improvements described below see the README_relnotes file in the main MORGAN directory.

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 for MORGAN 2.9. 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.

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.

In MORGAN V_2.6 (June 2004) there was further development of the Autozyg LM-sampler programs, including a new program lm_pval. There was more flexibility in specification of traits and markers to be used in an analysis, and of hypothesized trait locations in lod score programs. There were major changes in output format, making program more user-friendly. Almost all main programs and all subroutine libraries except CMF and Rans had some changes. There were new data structures.

MORGAN 2.5 (released November 2002) extended MORGAN 2.4.1, with the introduction of two new Autozyg programs for the MCMC estimation of multipoint lod scores, lm_markers and lm_bayes. There was additional enhancement of the new test examples, and the Autozyg/Test_2.5 directory is replaced by Autozyg/Gold2. The Genedrop directory was reorganized, and now includes the ibddrop program.
Additional improvements in MCMC startup and sampling were included, including burn-in options for all Autozyg MCMC programs. The sampling libraries were reorganized, with a single Sample library replacing Msample and Lsample, and the marker and chromosome linkage set-up routines being moved to the new Markers library.
There are now options to install the MORGAN programs on Windows PCs using MinGW or Cygwin compilers.
New trait specifications foreshadowing future complex trait model developments are also included.

MORGAN 2.4.1 (released June 2002) was a cleaned-up version of MORGAN 2.4, which included the programs ibddrop and kin, resurrected from the MORGAN 2.3.2 programs sim_ibd_link and autolink, respectively. New more realistic simulated test data sets were included for the Autolink programs, and new trait specifications for future complex trait development were incorporated.
Bug fixes for Nghds/input_ped and Quant input_data were released in July 2002

MORGAN 2.4 released February 2002: The functionality of all programs continues to improve, though most users will see little external change in this version. Character identifiers of individuals are permitted, and this has led to major reorganization and improvement of lower-level code. Although version 2.3.2 remains available for use with older parameter files, a switch to version 2.4 is strongly recommended.

MORGAN 2.3.2 released September 2001: The Autozyg programs now have an option to use sequential imputation for initialization. Autozyg/lm_auto now permits multiple proband gamete sets for scoring. The Msampler library contains improved version of the routine for marker locus penetrances. Fixed length arrays still in some programs have been replaced, resulting in improved efficiency of memory usage, allowing larger data sets. The documentation and gold standard reflect the new options.

MORGAN 2.3.1 bug of potential problem to Solaris and cygwin (PC) users, fixed, May 25, 2001.

MORGAN 2.3.1 (released April 2001) is an updated version of MORGAN 2.3. The Makefiles have been extensively revised, and the Fortran subroutine library eliminated. Additionally, a number of small improvements to programs ahave been made, particularly to the Autozyg programs.

MORGAN 2.3 (released December 2000): In addition to earlier programs of MORGAN 2.2 (released April 2000) MORGAN V2.3 contains improved versions of the MORGAN V1.1.2 (July 1999) programs for estimation of posterior probabilities of IBD among sets of 6 to 8 haplotypes, and MCMC estimation of multipoint lod scores, as described, for example, by Thompson (ISR (2000), 68: 53--73), using the LM-sampler (Heath and Thompson, AJHG 61 (Suppl.) A278).
MORGAN 2.3 contains two additional main program directories (Autozyg and Sim_IBD_link) and two libraries for MCMC sampling of inheritance vectors, either by locus (Lsample) or by meiosis (Msample).

Version 2.2 of the MORGAN software, released April 2000, replaced MORGAN 2.1. MORGAN_V2.2 contained four main program directories (PolyEM, Genedrop, Checkers, Testers) and eight libraries (CMF, Nghds, Quant, Rans, Stuff, Pars, Pedchk, Peel) in addition to Header files, Makefiles, documentation, and test data and output.

MORGAN_V2.2 had extensive reorganization of Header files and global variables from MORGAN 2.1 (released May 1999). It included also new programs for checking and reordering pedigrees (Checkers, Pedchk).

MORGAN 2.0.1 was a slightly updated version released February 1998, of version 2.0 (released November 1997). MORGAN 2.0.x contained only four core libraries and one main-program directory. This was the start of a new release of MORGAN with much improved user interface, and many other program improvements.



MORGAN Version 1.1

Monte Carlo Genetic Analysis

The 1.x development series of MORGAN has been superceded by MORGAN 2.3 . While we continue to have additional program and subroutine libraries in development that are not released, these will in the future be added into releases of MORGAN 2.x, which has a more friendly user interface.

The name MORGAN replaces the earlier provisional name of "Gibbs" . Thus MORGAN Version 1.1 was the May 1997 update of Gibbs Version 1.0 which was made available July 1996.

MORGAN 1.1.1, installed July 1997, contained only minor changes from MORGAN 1.1, for most programs.

MORGAN Version 1.1.2, made available July 1999. This contained additional MCMC programs that are now available in MORGAN 2.3.

The next update of the MORGAN programs will include additional improvements to Monte Carlo likelihood computations, and perhaps also a version of the age-of-onset program directory of Dr. Hongzhe Li.