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Bioinformatics. 2005 May 1;21(9):2123-5. Epub 2005 Jan 12.

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

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Bioinformatics Department, Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine Berlin-Buch, Germany.



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(R) 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.


ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see

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