Function
sumOfPairsScore
Given a multiple alignment, this function calculates the sum-of-pairs score.
sumOfPairsScore(graph, score_type)
Parameters
graph
An alignment graph.
Types: Alignment Graph
score_type
A score object.
Types: Score
Return Values
void
Remarks
This function does NOT assume independent columns. That is, gap openings are properly scored. If you want the fast version assuming independ columns use sumOfPairsScoreInd.
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