JPSGCS

Java Programs for Statistical Genetics and Computational Statistics

1 General information
2 Program information
3 Obtaining the software
4 File formats
5 Funding acknowledgments

General information

This is the home page for the documentation of programs written mostly by Alun Thomas at the Genetic Epidemiology Division of the University of Utah. These programs have been developed since 2002 to address problems in statistical genetics. However, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models.

The programs are written in Java version 1.5 and were developed in a Linux environment. However, they have also been successfully run without recompilation on Macs and PCs.

In March 2010 a major rewrite of the graphical modeling and Markov chain Monte Carlo was completed. This resulted in speeding up many of these programs, in some cases by a factor of up to 100. The biggest effect will be on programs handling large data sets or complex, looped pedigrees.

Program information

There are several ways that you can access information about the individual programs:

Access programs by name

An alphabetical list of all the top level programs included in the download.

Access programs by function

Programs listed by overlapping areas of application.

Access programs by publication

Here is a list of publications that describe or make use of programs available here.

Javadocs API

You can also browse the application programming interface generated directly from the source code using Javadocs.

Source code

The source code is included in the download and can also be read online.

Obtaining the software

You can download JPSGCS.jar a single jar, or Java archive, file containing all the available programs and packages. You can also get installation instructions.

Current information about the compilation date and the Java version used to compile the programs is given here.

File formats

In order to avoid propagating the already over abundant file formats used to convey genetic information such as model parameters, pedigree structure, and genotype data, we have made extensive use of the LINKAGE programs file format. While this is not always ideal, it is generally well used and understood, and in most cases it conveys a super set of the information we need. We have at times taken liberties with the format.

Funding acknowledgments

Much of this work was funded by grant awarding bodies whose support we gratefully acknowledge .