Current and future MORGAN developments: August 2007.
Updated March and August 2008, March 2009

MORGAN V2.8.1 was released in April 2006, and MORGAN V2.8.2 in April 2007. MORGAN V2.8.3 was released March 2008 and MORGAN V2.9 in August 2008.

A preliminary version of MORGAN-3, containing only the PedComp, Genedrop, and Autozyg programs, was released in March 2008. The full version of the package (including two new programs) is released March 2009, although it remains a beta-test version with much testing and documentation remaining to be done.

The current MORGAN Tutorial and Examples released in August 2007 are based on MORGAN 2.8.1. We therefore here detail developments of MORGAN 2.8.2 and MORGAN 2.8.3, as well as upcoming changes, and the development of MORGAN 3.0. The information is taken from the Future directions section of the 2007 MORGAN Tutorial. The information remains pertinent to MORGAN 2.9.

1. General Library functions:

Only functions affecting general MORGAN capabilities or enabling new programs are listed here. Many other general improvements in Morgan library functions and MORGAN set-up routines have been made. Some details may be found in MORGAN web release notes, or in the `README_relnotes' of each MORGAN release.

2. Autozyg programs:

3. LR_Lods programs:

To make room for new Lodscore programs being released in MORGAN V2.8.2, 2.8.3 and 3.0, the two older programs `lm_schnell' and `lm_lods' have been moved to the new directory LR_Lods. These two programs differ in several ways from newer programs, but the principal one is that they use the methods of combining likelihood ratios (LR) along the chromosome in order to estimate lod scores (see Thompson & Guo, 1991, IMA J Math Appl in Med & Biol).

The Gold1 subdirectory remains temporarily, since it provides the only tests of MCMC samplers on looped pedigrees. Gold1 `lm_lods' gold standards were omitted from the released MORGAN V2.8.2, due to delays in checking looped pedigree peeling routines: they will be reinstated in MORGAN V2.8.3.

4. Lodscore programs:

5. MORGAN 3.0 (release-2; March 2009) and two new programs

In March 2009, a full version of the MORGAN package using the MORGAN-3 "tloc" structures for trait loci is released. All MORGAN-2 programs, including lm_twoqtl, are included in this new release. The program `lm_twoqtl' allows two (linked or unlinked) quantitative trait loci to contribute additively or epistatistically to a single trait (see Sung et al., 2007, Genetic Epidemiology 31: 103-114).

Additionally there are two new programs:
1) The Autozyg program "gl_auto" is a more general version of the original lm_auto MORGAN program (which is still included in the package). The gl_auto program provides full lm_auto capabilities with the componentwise multiple-meiosis sampling of the lm_multiple program. Additionally it permits output of joint realizations of meiosis indicators or founder genome labels (hence "gl") sampled conditionally on marker data. These realizations may be used in subsequent analyses of trait data using a variety of trait models (e.g.)
2) The PedComp program "translink" also takes lm_auto style input but performs no genetic analyses. This program produces a pedigree file pedfile.dat and output file datafile.dat in LINKAGE format, in accordance with the pedigree, trait, marker, maps and models specified in the MORGAN parameter file, in order that other software can be more easily run using the same or eqivalent input information.