  We introduce a new heuristic for the multiple alignment of a set of
sequences. The heuristic is based on a set cover of the residue alphabet of the
sequences, and also on the determination of a significant set of blocks
comprising subsequences of the sequences to be aligned. These blocks are
obtained with the aid of a new data structure, called a suffix-set tree, which
is constructed from the input sequences with the guidance of the
residue-alphabet set cover and generalizes the well-known suffix tree of the
sequence set. We provide performance results on selected BAliBASE amino-acid
sequences and compare them with those yielded by some prominent approaches.

Quantitative Methods