BALSA - Bayesian Algorithm for Local Sequence Alignment
BALSA is a Bayesian algorithm for local sequence alignment that takes into account the uncertainty associated with all unknown variables by incorporating in its forward sums a series of scoring matrices, gap parameters and all possible alignments.

Bayesian Phylogenetic Footprinting
The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. The Bayesian Phylogenetic Footprinter bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest.