ON CALCULATING THE PROBABILITY OF A SET OF ORTHOLOGOUS SEQUENCES Junfeng Liu1, Liang Chen2, Hongyu Zhao3, Dirk F. Moore1, Yong Lin1 and Weichung Joe Shih1 1 Biometrics Division, CINJ-UMDNJ, USA, 2 Department of Biological Sciences, University of Southern California, USA. 3 Department of Epidemiology and Public Health, Yale University School of Medicine, USA. ABSTRACT: Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, we investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA sequences which evolve from a common progenitor. We propose Monte Carlo integration algorithms to sample the unknown ancestral and/or root sequences a posteriori conditional on a reference sequence and apply pairwise Needleman-Wunsch alignment (1970) between the sampled and non-reference species sequences to estimate the probability. We apply our algorithms to a set of CREB promoters among Human, Mouse and Rat.