Bayesian Bioinformatics Applications
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.
Gibbs Motif Sampler
The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.