[BioC] difference results by needle program and pairwiseAlignment

[Wang Peter]

thank you very much
it should be
scorem[i,j]=pairwiseAlignment(sequences[[i]], sequences[[j]], type =
"overlap", substitutionMatrix = "BLOSUM62", gapOpening = -9.5,
gapExtension = -0.5,scoreOnly=T)

i think

"overlap" solves (Needleman-Wunsch) global alignment,