How are the pairwise alignment scores generated?

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How are the pairwise alignment scores generated?

A pairwise score is calculated for every pair of sequences that are to be aligned. These scores are presented in a table in the results. Pairwise scores are calculated as the number of identities in the best alignment divided by the number of residues compared (gap positions are excluded). Both of these scores are initially calculated as percent identity scores and are converted to distances by dividing by 100 and subtracting from 1.0 to give number of differences per site. We do not correct for multiple substitutions in these initial distances.

As the pairwise score is calculated independently of the matrix and gaps chosen, it will always be the same value for a particular pair of sequences.

Alignment score is calculated in two ways - fast and slow (more accurate mode). The scores are calculated from separate pairwise alignments. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate).