Quality of alignment. Despite the central r le that alignment programs play in sequence analysis, a thorough analysis of the quality of methods based on statistically significant numbers of proteins has yet to be accomplished. Stability of alignment. Not necessarily, the reason may, as well, be that the alignment is just not unique, i.e., the best and the second best solution to the alignment problem may have similar scores. In such cases the alignment is less reliable in regions where the results from A and B differ.
Sequence alignments reveal underlying evolutionary processes.
Aligning protein sequences may appear to be purely a problem of matching letters. However, sequence alignments unravel information about structural and functional relations between residues in different proteins. Obviously it is not trivial to map the complexity of factors determining protein structure and function onto 1D relations between letters. Evolutionary divergence within sequence families. In general, regions with many insertions and deletions in the alignment are less informative.