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VTC author , David Ludwig , begins the tutorial by covering the basics of Sonar installation , tweaking Windows XP for optimization , and exploring the interface . The proof method supports the designer 's intuitive reasoning ; `` local '' argumentations , which are typical for incremental design and for optimizations , are supported by the semantical modularity of the design and proof method . Following the presentation of this code , the notes include several suggestions for optimizations to make it run faster . It also explains possible attacks and their solutions regarding the mechanisms used for optimization . David has developed models for horizontal gene transfer , and methods for optimization of trees and rapid bootstraps . A Hybrid Genetic Algorithm ( HGA ) was used for optimization .