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

Bioinformatics. 2005 May 1;21(9):2123-5. doi: 10.1093/bioinformatics/bti264. Epub 2005 Jan 12.


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(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.

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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosome Mapping / methods*
  • Computer Graphics
  • DNA Mutational Analysis / methods*
  • Gene Frequency
  • Genetics, Population / methods
  • Humans
  • Linkage Disequilibrium / genetics*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Software*
  • User-Computer Interface*