Master of Science (MS)
Traditional Multiple Sequence Alignment (MSA) Algorithms are deterministic. Genetic algorithms for protein MSA have been documented. However, these are not able to exceed in all cases the scores obtained by ClustalW, the freely available defacto standard. My solution, called “MSG”, places gaps rather than amino acids. The algorithm is multitribal, uses only a few very simple operators with adaptive frequencies, and jumpstarts one population from the ClustalW solution. Results are reported for 14 data sets, on all of which MSG exceeds the ClustalW score.
Heller, Philip, "MSG: A Gap-Oriented Genetic Algorithm for Multiple Sequence Alignment" (2009). Master's Projects. 141.