  We propose a new procedure for clustering nucleotide sequences based on the
"Laplacian Eigenmaps" and Gaussian Mixture modelling. This proposal is then
applied to a set of 100 DNA sequences from the mitochondrially encoded NADH
dehydrogenase 3 (ND3) gene of a collection of Platyhelminthes and Nematoda
species. The resulting clusters are then shown to be consistent with the gene
phylogenetic tree computed using a maximum likelihood approach. This comparison
shows in particular that the clustering produced by the methodology combining
Laplacian Eigenmaps with Gaussian Mixture models is coherent with the phylogeny
as well as with the NCBI taxonomy. We also developed a Python package for this
procedure which is available online.
