PPT Slide
Multiple alignment in 2002
The most widely used progressive alignment algorithm is currently CLUSTAL W, and we discuss this in detail below.
There are a number of more specialized procedures based on quite different principles, including the use of hidden Markov models built for protein families. We’ll discuss these briefly in the next lecture.
A relatively new and very promising approach uses Markov chain Monte Carlo methods to sample alignments according to certain probabilistic procedures and, by moving randomly around in the huge space of possible alignments, to find good alignments. We’ll give references to one of these.