Abstract: The mixed algorithms of genetic algorithms and simlutated annealing algorithm are put forward.The new algorithm not only sufficiently exerts the advantages of the two algorithms,but also improves the computing precision and speed.The algorithm simulates the recurrence of nature evolution process,and solves the contradiction between the diversity of population and the convergence speed.The experiment shows that the algorithm is effective.

Key words: multiple sequence alignment；bioinformatics, genetic algorithm；operator