  The way for performing multiple sequence alignment is based on the criterion
of the maximum scored information content computed from a weight matrix, but it
is possible to have two or more alignments to have the same highest score
leading to ambiguities in selecting the best alignment. This paper addresses
this issue by introducing the concept of joint weight matrix to eliminate the
randomness in selecting the best multiple sequence alignment. Alignments with
equal scores are iteratively rescored with the joint weight matrix of
increasing level (nucleotide pairs, triplets and so on) until one single best
alignment is eventually found. This method for resolving ambiguity in multiple
sequence alignment can be easily implemented by use of the improved scoring
matrix.
