These diagonals are the ones with most matches and are hence the most interesting for an alignment. Increasing this parameter will speed up the alignments but will result in more scores of zero. After the diagonals with most matches are found, this parameter specifies a window around each that will be used in the alignment. Decreasing this parameter will speed up the alignments. Percentage scores are advisable if the lengths differ greatly.
Absolute scores are better otherwise.
These parameters control the final multiple alignment. There are 2 gap penalty parameters and 1 for whether transitions are weighted in DNA alignments. The basic algorithm used, attempts to minimise the distance between groups of sequences. For amino acids, a Dayhoff PAM matrix is used. This parameter is a penalty for every gap that is introduced, regardless of length of gap.