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SHIPS (Spectral Hierarchical clustering for the Inference of Population Structure) is a nonparametric clustering algorithm that clusters individuals from a population into genetically homogeneous subpopulations from genotype data. After computing a pairwise distance matrix, the algorithm progressively divides the original population in two subpopulations by the use of a spectral clustering algorithm. The process is then iterated in each of the two subpopulations and so on. This leads to the construction of a binary tree, where each node represents a group of individuals. To determine the final clusters a tree pruning procedure and an estimation of the optimal number of clusters, that is a gap statistic, are applied. In such an approach both the final clustering of the individuals and the number of clusters are estimated by the method.
The algorithm SHIPS is implemented with the software R that can be downloaded from the (CRAN web page) and is divided in several functions :