Heuristic alignment methods

Abstract

Computation of multiple sequence alignment (MSA) is usually formulated as a combinatory optimization problem of an objective function. Solving the problem for virtually all sensible objective functions is known to be NP-complete implying that some heuristics must be adopted. Several general strategies have been proven effective to obtain accurate MSAs in reasonable computational costs. This chapter is devoted to a brief summary of most successful heuristic approaches. © 2014 Springer Science+Business Media, LLC.