Stochastic evolution and multifractal classification of prokaryotes

Proc. SPIE 5110, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems, Ed. Sergey M. Bezrukov, Hans Frauenfelder and Frank Moss, Santa Fe, USA, June 2003, pp192-200 We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the model to mimic large scale genomic changes, and use this to evaluate multifractal and related information theory techniques which take into account these large changes in determining phylogenetic relationships.