The problem of simultaneously aligning a number of sequences is referred to as multiple sequence alignment. We provide a dynamic programming algorithm for multiple alignment which extends the dynamic programming algorithm for global pairwise alignment. We describe frequency based algorithms to align a sequence against a multiple alignment and to align a multiple alignment against another multiple alignment. We introduce the method of 3D profile alignment that allows to align an amino acid sequence against a tertiary protein structure. This method is useful for tertiary structure prediction. As the dynamic programming algorithm for multiple sequence alignment is very time consuming, we provide a useful approximation algorithm and discuss the heuristic method of progressive alignment.