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src/c/o/cogent-1.5.3/tests/test_align/test_align.py   cogent(Download)
                                 mprob_model='conditional')
        tree = cogent.LoadTree(tip_names=['A', 'B'])
        lf = codon_model.makeLikelihoodFunction(tree, aligned=False)
        lf.setSequences(dict(A=s1, B=s2))
        (score, a) = lf.getLogLikelihood().edge.getViterbiScoreAndAlignment()

src/p/y/pycogent-HEAD/tests/test_align/test_align.py   pycogent(Download)
                                 mprob_model='conditional')
        tree = cogent.LoadTree(tip_names=['A', 'B'])
        lf = codon_model.makeLikelihoodFunction(tree, aligned=False)
        lf.setSequences(dict(A=s1, B=s2))
        a = lf.getLogLikelihood().edge.getViterbiPath().getAlignment()