AutoSNP 

Method for SNP detection using SNP redundancy score and co-segregation . The frequency of occurrence of a polymorphism at a particular locus provides a measure of confidence in the SNP representing a true polymorphism and is referred to as the SNP redundancy score. In addition, true SNPs that represent divergence between homologous genes co-segregate to define a conserved haplotype. A co-segregation score based on whether a SNP position contributes to defining a haplotype is a further independent measure of SNP confidence. The SNP score and co-segregation score to-gether provide a valuable means for estimating confidence in the validity of SNPs within aligned sequences independent of sequence trace files. Two methods currently apply a combination of redundancy and haplotype co-segregation; autoSNP (Barker et al, 2003, Batley et al, 2003)\, and SNPServer (Savage et al, 2005) (http://www.appliedbioinformatics.com.au/index.php/SNP_discovery)