Bayes Aligner is a bayesian adaptive sequence alignment algorithms.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. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data.
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Zhu, J.;Liu, J.S.; Lawrence, C.E.
Bayesian adaptive sequence alignment algorithms.
Bioinformatics 14:25-39, 1998