Software

JLIN: A java based linkage disequilibrium plotter

Kim W Carter^1* , Pamela A McCaskie^1,2* and Lyle J Palmer^1,2

¹  Laboratory for Genetic Epidemiology, Western Australian Institute for Medical Research and UWA Centre for Medical Research, University of Western Australia, Nedlands, 6009, Western Australia

²  School of Population Health, University of Western Australia, Nedlands, 6009, Western Australia

author email corresponding author email* Contributed equally

BMC Bioinformatics 2006, 7:60doi:10.1186/1471-2105-7-60

Published:	9 February 2006

Abstract

Background

A great deal of effort and expense are being expended internationally in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Techniques such as Linkage Disequilibrium mapping are being increasingly used to examine and compare markers across increasingly large datasets. Visualisation techniques are becoming essential to analyse the ever-growing volume of data and results available with any given analysis.

Results

JLIN (Java LINkage disequilibrium plotter) is a software package designed for customisable, intuitive visualisation of Linkage Disequilibrium (LD) across all common computing platforms. Customisation allows the user to choose particular visualisations, statistical measures and measurement ranges. JLIN also allows the user to export images of the LD visualisation in several common document formats.

Conclusion

JLIN allows the user to visually compare and contrast the results of a range of statistical measures on the input dataset(s). These measures include the commonly used D' and r² statistics and empirical p-values. JLIN has a number of unique and novel features that improve on existing LD visualisation tools.