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src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
        t = LoadTree(treestring="(a,c);")
        sm = substitution_model.Dinucleotide(mprob_model='tuple')
        lf = sm.makeParamController(t)
        lf.setAlignment(al)
        simalign = lf.simulateAlignment()
        def use_root_seq(root_sequence):
            al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
            t = LoadTree(treestring="(a,c);")
            sm = substitution_model.Dinucleotide(mprob_model='tuple')
            lf = sm.makeParamController(t)

src/c/o/cogent-1.5.3/tests/test_evolve/test_likelihood_function.py   cogent(Download)
        t = LoadTree(treestring="(a,c);")
        sm = substitution_model.Dinucleotide(mprob_model='tuple')
        lf = sm.makeParamController(t)
        lf.setAlignment(al)
        simalign = lf.simulateAlignment()
        def use_root_seq(root_sequence):
            al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
            t = LoadTree(treestring="(a,c);")
            sm = substitution_model.Dinucleotide(mprob_model='tuple')
            lf = sm.makeParamController(t)