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MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

Tom R Gaunt1*†, Santiago Rodriguez1†, Carlos Zapata2 and Ian NM Day1

Author Affiliations

1 Human Genetics Division, University of Southampton, School of Medicine, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK

2 Departamento de Genética, Universidad de Santiago, Santiago de Compostela, Spain

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BMC Bioinformatics 2006, 7:227 doi:10.1186/1471-2105-7-227

Published: 27 April 2006

Abstract

Background

Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form.

Results

We have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection.

Conclusion

MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.

Availability

Available from http://www.genes.org.uk/software/midas webcite and http://www.sgel.humgen.soton.ac.uk/midas webcite