matches2gappedSeqs (
        matches,
        s1,
        s2,
        gapChar=None,
        reverseSorts=None,
        )

cloneSeq ( seq )

nw (
        s1,
        s2,
        scoreMatch=None,
        scoreMismatch=None,
        scoreGap=None,
        scoreGapOpen=None,
        gapChar=None,
        returnSeqs=None,
        scoreMatrix=None,
        similarityMatrix=None,
        frequencyMatrix=None,
        endsAreGaps=None,
        ssMatrix=None,
        ssFraction=None,
        gapOpenHelix=None,
        gapOpenStrand=None,
        gapOpenOther=None,
        debug=None,
        )