BSA is a huge field since sequences are presently so abundant. So far Jotun has covered pairwise and multiple alignment optimizing some score function or defined via a heuristic algorithm. In this lecture Jotun will cover the use of HMMs (Profile, Pairwise, Phylogenetics) as invented in the 90s. Then, Jotun will discuss sequence comparison, that does not need an alignment (alignment free methods). A finish with local alignment, probability theory of sequence comparison and database search.
Preliminary slides can be found here.