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Flowcharts of data processing for pair-wise linkage analysis employing MLINK or Superlink by SNP HiTLink. In Windows OS, import of SNP data, generation of allele frequency file, annotation file and lkin file are conducted along with selection of markers. After lkin file is transported to Unix OS, run_linkage.pl carries out continuous run of MLINK or Superlink by rewriting pedin.pre and pedin.dat files for each marker.
