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How to Use HAPAR If UNIX executable is downloaded, it needs to be decompressed first. Please use the following two commands in order to decompress.   (1) gunzip hapar.tar.gz   (2) tar xvf hapar.tar Now you get a file named hapar, which can be executed directly. Usage:    hapar inputfile Input file format: Input file contains the genotype data generated in experiment. The first line contains: genotype-number  SNP-number One genotype is represented by a consecutive sequence of SNP sites, and each SNP site can be 0 (for homozygous wild type), 1 (for homozygous mutant), or 2 (for heterozygote). A sample input file. Output file format: The reconstructed haplotypes are output in file hapar.out The first line contains: haplotype-number  SNP-number One haplotype is represented by a consecutive sequence of SNP sites, and each SNP site can be either 0 (for homozygous wild type) or 1 (for homozygous mutant). Then resolutions of the input genotypes are listed. Some genotypes may contain more than one possible resolution. A sample output file. Here is an example taken from real biological data: B2ar (B2-adrenergic receptor gene). Input file (B2ar.in) is as follows: 18 12 011100011101 120011100101 110011100101 110011120101 111011110020 212222222101 211222212202 112011120202 212222212101 222222222101 212222222202 112011120222 112011120201 212011100101 211011120202 211222212101 212222222202 110011100202 Run: HAPAR B2ar.in The output file is : 10 12 110011100000 011011100101 111011110001 111011110101 011100011101 100011100101 110011100101 110011110101 111011110000 111011110010 Resolution of input Genotypes: Genotype                   Resolution 011100011101:      011100011101 + 011100011101 ; 120011100101:      100011100101 + 110011100101 ; 110011100101:      110011100101 + 110011100101 ; 110011120101:      110011100101 + 110011110101 ; 111011110020:      111011110000 + 111011110010 ; 212222222101:      011100011101 + 110011100101 ; 211222212202:      011100011101 + 111011110000 ; 112011120202:      110011100000 + 111011110101 ; 110011100101 + 111011110000 ; 212222212101:      011100011101 + 110011110101 ; 222222222101:      011100011101 + 100011100101 ; 212222222202:      110011100000 + 011100011101 ; 112011120222:      110011100101 + 111011110010 ; 112011120201:      111011110001 + 110011100101 ; 212011100101:      011011100101 + 110011100101 ; 211011120202:      011011100101 + 111011110000 ; 211222212101:      111011110101 + 011100011101 ; 212222222202:      110011100000 + 011100011101 ; 110011100202:      110011100000 + 110011100101 ;