Parameter Advising for Multiple Sequence Alignment

This book develops a new approach called parameter advising for finding a parameter setting for a sequence aligner that yields a quality alignment of a given set of input sequences. In this framework, a parameter advisor is a procedure that automatically chooses a parameter setting for the input, and has two main ingredients:

(a) the set of parameter choices considered by the advisor, and

(b) an estimator of alignment accuracy used to rank alignments produced by the aligner.

On couplin...