AlignedXStringSet-class
                        AlignedXStringSet and QualityAlignedXStringSet
                        objects
InDel-class             InDel objects
PairwiseAlignments-class
                        PairwiseAlignments,
                        PairwiseAlignmentsSingleSubject, and
                        PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io   Write a PairwiseAlignments object to a file
align-utils             Utility functions related to sequence alignment
pairwiseAlignment       Optimal Pairwise Alignment
phiX174Phage            Versions of bacteriophage phiX174 complete
                        genome and sample short reads
pid                     Percent Sequence Identity
predefined_scoring_matrices
                        Predefined scoring matrices
stringDist              String Distance/Alignment Score Matrix
substitution_matrices   Utilities to generate substitution matrices
