Epistasis analysis is an essential tool of classical genetics for inferring the order of function of genes in a common pathway. Typically, it considers single and double mutant phenotypes and for a pair of genes observes whether a change in the first gene masks the effects of the mutation in the second gene. Despite the recent emergence of biotechnology techniques that can provide gene interaction data on a large, possibly genomic scale, few methods are available for quantitative epistasis analysis and epistasis-based network reconstruction.