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The fastcluster package is a C++ library for hierarchical, agglomerative clustering. It provides a fast implementation of the most efficient, current algorithms when the input is a dissimilarity index. Moreover, it features memory-saving routines for hierarchical clustering of vector data. It improves both asymptotic time complexity (in most cases) and practical performance (in all cases) compared to the existing implementations in standard software: several R packages, MATLAB, Mathematica, Python with SciPy.
Daniel Müllner (Tue,) studied this question.