There are indeed quite a few multiple alignment algorithms. Wallace et al counted around 50. They started drawing trees of alignment algorithms.
Has anyone collected a list of all papers that developed a new alignment algorithm (each one, of course, better than a couple of the others)? I personally would bet that - given that the number of algorithms raise with algorithmical simplicity and the interpretability of the results - motif discovery on DNA is one of the disciplines that generated the most different papers about a new algorithm (counted around 80). Fortunately, the decision is much simpler as the savvy bio-computerfreak knows: With so much choice, the first program that gently compiles after "make" has a good chance of getting used in the end. Is this the reason why everyone is using BLAST today? Or was that a completely different time?
