MORGAN 3.4 is released in December 2017:
Various capabilities were added to gl_lods and fgl2haplo programs, and to marker selection and age-dependent liability penetrances. A more major set of changes provide dense marker versions of both ibddrop and markerdrop (these also required changes to fgl2haplo, fgl2ibd and fgl2dgl). The new ibddrop supercedes the simped_fgl program, which is removed from ibd_create. The ibddrop program runs with or without a tloc, as also gl_auto, and various changes were made to clarify this usage. There is a new beta-test option to impose genetic selection at the tloc in ibddrop, and a new beta-test version of ibd_haplo to run on parent-offspring trios (ibd_trios).

MORGAN 3.3.2 is released in July 2016: (and temporarily remains available above).
Further changes have been made in the base-pair vs centiMorgan set-up in some ibd_create subprograms: There are two new fgl2dgl gold standards demonstrating this change. A new program, base_trait_lods, was added to the Lodscore directory. This program computes the trait-data probability for each component in a pedigree, either by pedigree peeling or by Monte Carlo integration. Other minor changes include a rewording of parameter statements, so that, in the context of Monte Carlo, "MC" now refers only Markov chain Monte Carls.

MORGAN 3.3.1 is released in February 2016:
The major change is in improvements to ibd_create, including the addition of two new subprograms, simped_fgl and fgl2dgl. Additional capabilities were also added to ibd_haplo and gl_lods. Also changes were made to the computation of trait likelihoods on fgl graphs, to reduce the chance of underflow, and several changes were made to improve memory management in MORGAN programs.

MORGAN 3.3 is released in May 2015:
The major change is in the addition of a suite of 5 subprograms under the program ibd_create. These five subprograms are simpop_fgl, beaglesim, beagledag, fgl2ibd and fgl2haplo, and they serve to generate genetic data on population-based samples of related indiviuals which can then be used in testing of other methods:
(1) simpop_fgl simulates a population pedigree, and the descent of fgl segments within that pedigree; (2) beaglesim simulates haplotypes from a BEAGLE DAG model. Where this model has been fit on real data, realistic haplotypes result; (3) beagledag is a preliminary prototype program that parses the BEAGLE DAG model, and computes local haplotype frequencies; (4) fgl2ibd takes the FGL output of simpop_fgl and scores ibd patterns at selected marker positions across the chromosome; (5) fgl2haplo takes the same FGL output, but combines it with population haplotype information from beaglesim (or from another source) to create a data set of haplotypes in related individuals in population samples.
The addition of example Gold standards for these new programs has led to a three-fold increase in the size of the MORGAN package; we aim to provide smaller Gold standard files in future, but generally for realistic examples, these programs have large input files and generate large output files.
Other smaller changes have been made througout MORGAN, to clean up internal handling of data. Additionally, the use of liability penetrances has been updated, so that information for this trait type is now enetered via regular MORGAN parameter statements. This permits the gl_lods program to use this trait type.

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.

Online version of the tutorial (paginated html)

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.

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.