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        "description": "=========\nAlignment\n=========\n\nAlignment is a native Python library for generic sequence alignment. It is\nuseful in cases where your alphabet is arbitrarily large and you cannot use\ntraditional biological sequence analysis tools. It supports global and local\npairwise sequence alignment. I also plan to add support for profile-profile\nalignments, but who knows when.\n\nInstallation\n============\n\nYou can install the most recent release using pip:\n\n    pip install alignment\n\nUsage\n=====\n\nTypical usage looks like this::\n\n    from alignment.sequence import Sequence\n    from alignment.vocabulary import Vocabulary\n    from alignment.sequencealigner import SimpleScoring, GlobalSequenceAligner\n\n    # Create sequences to be aligned.\n    a = Sequence('what a beautiful day'.split())\n    b = Sequence('what a disappointingly bad day'.split())\n\n    # Create a vocabulary and encode the sequences.\n    v = Vocabulary()\n    aEncoded = v.encodeSequence(a)\n    bEncoded = v.encodeSequence(b)\n\n    # Create a scoring and align the sequences using global aligner.\n    scoring = SimpleScoring(2, -1)\n    aligner = GlobalSequenceAligner(scoring, -2)\n    score, encodeds = aligner.align(aEncoded, bEncoded, backtrace=True)\n\n    # Iterate over optimal alignments and print them.\n    for encoded in encodeds:\n        alignment = v.decodeSequenceAlignment(encoded)\n        print alignment\n        print 'Alignment score:', alignment.score\n        print 'Percent identity:', alignment.percentIdentity()\n        print\n\nTODO List\n=========\n\n- Profile-profile alignment is not working yet.",
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