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Bioinformatics Advance Access originally published online on July 12, 2005
Bioinformatics 2005 21(17):3565-3567; doi:10.1093/bioinformatics/bti571
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

easyLINKAGE-Plus—automated linkage analyses using large-scale SNP data

K. Hoffmann 1 and T. H. Lindner 2,3,*

1Institute of Medical Genetics, Charité, Humboldt University Berlin Augustenburger Platz 1, 13353 Berlin, Germany
2Division of Nephrology, Department of Medicine, Medical University Clinic at the University of Würzburg Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
3Department of Clinical Biochemistry and Pathobiochemistry, Medical University Clinic at the University of Würzburg Versbacher Strasse 5, 97078 Würzburg, Germany

*To whom correspondence should be addressed.

Summary: We extended the original easyLINKAGE program by enabling linkage analyses for large-scale SNP data in addition to those of microsatellites. We implemented new modules for Allegro, Merlin, SimWalk, GeneHunter Imprinting, GeneHunter TwoLocus, SuperLink and extended FastSLink by automatic loop breaking and new outputs. We added conditional linkage analyses as well as multipoint simulation studies, and extended error test routines by checking for Mendelian/non-Mendelian genotyping errors and for deviations from Hardy–Weinberg equilibrium. Data can be analyzed in sets of markers, in defined centimorgan intervals and by using different allele frequency algorithms. The outputs consist of genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P-values and other parameters.

Availability: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm

Contact: tom.lindner{at}mail.uni-wuerzburg.de

Supplementary information: Supplementary information is available on the website. The current version is v4.01beta.

Received on March 2, 2005; revised on June 15, 2005; accepted on July 3, 2005

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