Optimization with Genetic Algorithm for Outcome of Multiple Sequence Alignments

Sequence alignment method refers to the residues column position arrangement of two or more sequences by removing or inserting vacancy in biology sequences file (protein or nucleic acid), which can obtain the correlation information between the sequences. The authors developed a kind of optimization package with genetic algorithm for outcome of MSA, which can initialize with random mode or seed mode, and improve the outcome of MSA with the selected fitness function as COFFEE, SPS or WSPS, and some other GA parameters as cross rate, mutation rate, substitution matrix and terminate condition. These improvements are very important to the subsequent analysis as genotyping, clustering of species, conserved motif discovery or mutation identification.