We have created an algorithm that converts integrated SNP and CNV calls generated from Birdsuite 's Fawkes procedure into phased copy number genotypes (CN genotypes) using familial pedigree data. This software makes possible the use of CNPs and CNVs for genetic linkage with family data. The application is platform independent and may be used by Linux, Windows and Mac users.

We have created a program that automatically generates the input files for the Alohomora_m software. The program Chip2Spell takes as input a genotype report and publicly available annotation files and creates the genotype file, map file and frequency file that will be used by Alohomora. The program is especially useful if the map and frequency files for a given plateform are not stored in the Alohomora library, but it is also a quick way to convert the standard Affymetrix or Illumina genotype report format to the AB format requested by Alohomora. The latest Affymetrix and Illumina whole genome plateforms are specifically supported, but it is also possible to use Chip2Spell with previous chips.