Data Analysis Software from the BRC

The following software for genetic data analysis were developed and made available by researchers at or affiliated with the Bioinformatics Research Center:

Alternative Splicing Gallery (ASG) GDA QTL Cartographer Windows QTL Cartographer Forensic DNA Mixtures

Hy-Phy PowerMarker Mixed Models and QTLs Exact Tests Cytonuclear Disequilibria

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Alternative Splicing Gallery (ASG) is a web-based splicing graph database that integrates transcript information from Ensembl, RefSeq, STACK, TIGR gene index, and UniGene, in order to explore and visualize gene structure and alternative splicing and to provide an exhaustive transcript catalog. The program was developed by Jeremy Leipzig and Dr. Steffen Heber.

Genetic Data Analysis (GDA) is a software package for analyzing discrete population genetic data. There are versions of GDA suitable for all Microsoft Windows platforms. The Lewis Lab Software Site has links for downloading the program over the web and instructions for downloading the program using anonymous FTP.

QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.

Windows QTL Cartographer maps quantitative trait loci in cross populations from inbred lines. It incorporates many of the modules found in its command-line sibling, QTL Cartographer (see above). WinQTLCart includes powerful graphic tools for presenting mapping results and can import and export data in a variety of formats.

DNAMIX v.3 calculates likelihood ratios for mixed DNA samples encountered in forensic science. It is platform-independent and is applicable to complex mixtures as well as single-contributor stains.

Hypothesis Testing Using Phylogenies (Hy-Phy) is a software package for maximum likelihood analyses of genetic sequence data. It is equipped with tools to test various statistical hypotheses.

PowerMarker, written by Jack Liu, is a comprehensive set of statistical methods for discrete genetic data analysis, designed especially for SNP/SSR data analysis. It also includes a 2-D Viewer and CoreSet batch system.

Mixed Models and QTLs: Programs for mixed model approaches for quantitative genetic analysis by Jun Zhu.

Exact conditional tests for different combinations of allelic and genotypic disequilibria on haploid and diploid data, or their combination. Get readme file, source code in UNIX archive, source code in MS-DOS archive, solaris2.6 executable, sgi-irix6.5 executable, MS Windows executable.

Cytonuclear Disequilibrium: Christopher J. Basten has written two programs for calculating cytonuclear disequilibria. These are MS Windows and Macintosh binaries as well as the UNIX distribution including source code and a makefile. All three distributions include example files and documentation. These programs have online manual pages.

For diallelic cytonuclear systems, see CNDd. For multiallelic systems, see CNDm.