AntMap

AntMap: Software for Constructing Genetic Linkage Maps using an Ant Colony Optimization Algorithm. Locus ordering is an essential procedure in genome mapping. When the number of loci is large, it is quite difficult to determine the optimum order. The problem of searching for the optimum order has been recognized as a special case of the traveling salesman problem (TSP). In recent years, Ant Colony Optimization (ACO), which is a methodology inspired by the behavior of real ant colonies, has been successfully used to solve TSP. We developed a novel system based on ACO for locus ordering against such a background. We tested the system using a simulated segregation population, and found it is highly efficient for linkage mapping. To commoditize our newly-developed system, we developed software named AntMap for constructing linkage map by the system. AntMap performs segregation test, linkage grouping and locus ordering, and constructs a linkage map quite rapidly and nearly automatically. With the aid of this software, researchers can save their time and labor, and can obtain a linkage map whose reliability is indicated by bootstrap values.

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  1. Julian Taylor, David Butler: R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis (2017) arXiv