Genetic linkage studies using whole genome scans are useful approaches for identifying genes related to human diseases. In general, these studies require genotyping of a large number of markers, which are used in statistical analysis. Recent technology has allowed easy genotyping of a large number of markers in less time; therefore, interface programs are required for manipulation of these large data sets. We present a new algorithm, which processes input data in LINKAGE format from data analyzed by automated genotyping systems. The algorithm was implemented in PERL script and R environment. Validation was performed with genotyped data from 127 individuals and 720 microsatellite markers of two whole genome scans. Our results showed a significant decrease in data processing time. In addition, this algorithm provides unbiased allele frequency estimation used for linkage analysis. LINKGEN is a freely available online tool and allows easier, faster, and reliable manipulation of large genotyping data sets.