Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures

We present Core Hunter, an advanced stochastic local search algorithm for selecting core subsets. Core Hunter is able to find core subsets having more genetic diversity and better average genetic distance than the current state-of-the-art algorithms for all genetic distance and diversity measures we evaluated. Furthermore, Core Hunter can attempt to optimize any number of genetic measures simultaneously, based on the preference of the user. Notably, Core Hunter is able to select significantly smaller core subsets, which retain all unique alleles from a reference collection, than state-of-the-art algorithms.Core Hunter is a highly effective and flexible tool for sampling genetic resources and establishing core subsets. Our implementation, documentation, and source code for Core Hunter is available at http://corehunter.org webciteGenetic resources stored in gene banks are usually sampled with the purpose of evaluating and utilizing them efficiently, as well as studying phenotypic and genotypic diversity, identifying duplicate accessions, and forming core subsets. The aim of the latter activity is to preserve in the sample as much of the diversity present in the original collection as possible. Core subset selection can be based on varying criteria including phenotypic traits or various forms of molecular marker data including, but not limited to, single nucleotide polymorphisms (SNP), amplified fragment length polymorphisms (AFLP), random amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR). A simple example considering SNP data is given in Figure 1. The concept of core collections (or core subsets) was introduced to increase the efficiency of characterizing and utilizing the collections stored in gene banks while preserving the genetic diversity of the collection [1,2].In many instances, gene bank curators and genetic resource conservation managers need to stratify their sampling procedure prior to forming a core subset. The criteria for stratifying sa