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Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):2123-2125; doi:10.1093/bioinformatics/bti264
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

ALOHOMORA: a tool for linkage analysis using 10K SNP array data

Franz Rüschendorf 1,2,* and Peter Nürnberg 2,3

1Bioinformatics Department, Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine Berlin-Buch, Germany
2Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine Berlin-Buch, Germany
3Cologne Center for Genomics, University of Cologne Cologne, Germany

*To whom correspondence should be addressed at Gene Mapping Center, Max Delbrück Center for Molecular Medicine (MDC), Berlin-Buch, Robert-Roessle-Strasse 10 13092 Berlin, Germany.

Summary: ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip® Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire dataset as well as for individual families.

Availability: ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/

Contact: fruesch{at}mdc-berlin.de


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