has_specified_input has_specified_input achieves_planned_objective gap creation penalty setting specification DNA substitution matrix gap extension penalty setting specification amino acid substitution matrix pairwise sequence alignment objective pairwise sequence alignment data transformation slow pairwise sequence alignment data transformation A pairwise sequence alignment data transformation that produces accurate alignments are carried out by using a dynamic programming method (Myers and Miller) to align every pair of sequences. ClustalW Documentation Ready for OBI-WS : v1.0 slow pairwise sequence alignment ITPPR