We develop an algorithm based on three basic DNA editing operations suggested by a model for ciliate micronuclear decryption, to transform a given permutation into another. The number of ciliate operations performed by our algorithm during such a transformation is taken to be the distance between two such permutations. Applying well-known clustering methods to such distance functions enables one to determine phylogenies among the items to which the distance functions apply. As an application of these ideas we explore the relationships among the chromosomes of eight fruitfly (drosophila) species, using the well-known UPGMA algorithm on the distance function provided by our algorithm.