Definitions for "Multiple alignment"
A Multiple Alignment of sequences is a rectangular array, consisting of characters taken from the alphabet A , that satisfies the following conditions: There are exactly rows; ignoring the gap character, row number is exactly the sequence s I ; and each column contains at least one character different from "-". In practice multiple sequence alignments include a cost/weight function, that defines the penalty for the insertion of gaps (the "-" character) and weights identities and conservative substitutions accordingly. Multiple alignment algorithms attempt to create the optimal alignment defined as the one with the lowest cost/weight score.
A multiple sequence alignment is a matrix of data, in which the individual columns represent homologous characters.
an alignment between three or more strings, whereas a pairwise alignment includes only two strings