InDel objects

Description

Starting with BioC 3.19, the following functions are defined in the pwalign package:

• writePairwiseAlignments

• nucleotideSubstitutionMatrix

• errorSubstitutionMatrices

• qualitySubstitutionMatrices

• insertion

• deletion

• unaligned

• aligned

• indel

• nindel

• PairwiseAlignments

• pattern

• alignedPattern

• alignedSubject

• PairwiseAlignmentsSingleSubject

• nedit

• mismatchTable

• mismatchSummary

• compareStrings

• pid

• pairwiseAlignment

• stringDist