matches2gappedSeqs (
        matches,
        s1,
        s2,
        gapChar=".",
        reverseSorts=True,
        )

cloneSeq ( seq )

nw (
        s1,
        s2,
        scoreMatch=10,
        scoreMismatch=-3,
        scoreGap=0,
        scoreGapOpen=-40,
        gapChar=".",
        returnSeqs=False,
        scoreMatrix=None,
        similarityMatrix=None,
        frequencyMatrix=None,
        endsAreGaps=False,
        ssMatrix=None,
        ssFraction=0.9,
        gapOpenHelix=None,
        gapOpenStrand=None,
        gapOpenOther=None,
        debug=False,
        )