def NW(string1, string2, gap = -1, match = 1, mismatch = -1):
    """Performs Needleman-Wunsch alignment of string1 and string2.
    Prints out the alignment and returns the array of scores and pointers(arrows).
    Example usage from an interactive shell:
    from NeedlemanWunsch import NW
    Scores, Pointers = NW('Pelican', Coelacanth')
    """
    # initialize scoring and 'arrow' matrices to 0
    Scores = [[0 for x in range(len(string2)+1)] for y in range(len(string1)+1)]
    Pointers = [[0 for x in range(len(string2)+1)] for y in range(len(string1)+1)]
    # initialize borders
    # for pointers (arrows), use 2 for diagonal, -1 for horizontal, and 1 for vertical moves.
    # I have tried to consistently use i for rows (vertical positions) in the score and pointer tables, and j for columns (horizontal positions).
    for i in range(len(string1)+1):
        Scores[i][0] = gap*i
        Pointers[i][0] = 1
    for j in range(len(string2)+1):
        Scores[0][j] = gap*j
        Pointers[0][j] = -1
    # fill with scores
    for i in range(1,len(string1)+1):
        for j in range(1,len(string2)+1):
            letter1 = string1[i-1]
            letter2 = string2[j-1]
            if letter1 == letter2: DiagonalScore = Scores[i-1][j-1] + match
            else: DiagonalScore = Scores[i-1][j-1] + mismatch
            HorizontalScore = Scores[i][j-1] + gap
            UpScore = Scores[i-1][j] + gap
            # TempScores is list of the three scores and their pointers
            TempScores = [[DiagonalScore,2],[HorizontalScore,-1],[UpScore,1]]
            # Now we keep the highest score, and the associated direction (pointer)
            Scores[i][j], Pointers[i][j] = max(TempScores)
    # backtrace from the last entry.  
    [i,j] = [len(string1),len(string2)]
    align1 = ''
    align2 = ''
    while [i,j] != [0,0]:
        if Pointers[i][j] == 2:
            align1 = align1 + string1[i-1]
            align2 = align2 + string2[j-1]
            i = i - 1
            j = j - 1
        elif Pointers[i][j] == -1:
            align1 = align1 + '-'
            align2 = align2 + string2[j-1]
            j = j - 1
        else:
            align1 = align1 + string1[i-1]
            align2 = align2 + '-'
            i = i - 1
    # the alignments have been created backwards, so we need to reverse them:
    align1 = align1[::-1]
    align2 = align2[::-1]
    # print out alignment
    print align1
    print align2
    # in case you want to look at the scores and pointers, the function returns them
    return [Scores,Pointers]