Figure 3From: Bayesian coestimation of phylogeny and sequence alignmentGenerating the proposal alignment. This figure illustrates the stochastic sequence aligner. In the deterministic fill-in process, the three scores are s1, s2 and s3, hence the value in this cell is max{s1, s2, s3}. In the stochastic traceback phase, the three neighbor cells are choosen with probabilities proportional to exp(αs i ), where α > 0 is a scaling parameter. The chosen traceback path corresponds to the proposed alignment in the usual way.Back to article page