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Core Hunter
Permits the selection of core collections. Core Hunter treats core selection as a formal optimization problem by directly sampling from the entire collection, optimizing a given diversity measure. It prevents the search stalling in local optima by using Replica Exchange Monte Carlo (REMC) search. This tool is able to build cores based on genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many provided evaluation measures depending on the precise purpose of the core.
GenoCore
Offers a method to select a core collection using modified statistical measures related to genetic allele coverage and diversity. GenoCore is an R package developed to select a core collection from large, diverse genetic datasets. It can be used for large datasets such as high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS). Compared with similar methods, GenoCore has a biggest minMR, so the minimum genetic distance between samples in the core collection is largest.
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