1. Computer storage media comprising instructions encoding a method of sequencing two or more different sequences, the method comprising: receiving mixed emissions data obtained from the two or more different sequences, the mixed emissions data having a plurality of distributions at a plurality of positions; determining peak amplitudes of the plurality of distributions to determine the plurality of positions corresponding to the plurality of distributions; and mapping at least some of the plurality of distributions and the corresponding positions of at least some of the plurality of distributions to the two or more different sequences according to a parametric model having parameters that are estimated utilizing overlapping, sliding windows of data from the mixed emissions data where cumulative data from previous windows of data serve as a prior for a current window of data, the mapping to sequence the two or more different sequences, the estimated parameters being used to model phase, amplitude and nucleotide information.