Adaptive Local Realignment

Mutation rates differ across the length of most proteins, but when multiple sequence alignments are constructed for protein sequences, a single alignment parameter choice is often used across the entire length. This chapter reviews an approach called adaptive local realignment which is the first method to compute protein multiple sequence alignments using diverse parameter settings for different regions of the input sequences. In this way, parameter choices can vary across the length of a protein to more closely model the local mutation rate.