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src/c/o/cogent-1.5.3/tests/test_evolve/test_coevolution.py   cogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel, Empirical
from cogent.app.gctmpca import gctmpca_aa_order,\
 default_gctmpca_aa_sub_matrix
        aa_freqs_3 = {'A':0.5,'C':0.3,'D':0.2}
        sm = Empirical(\
            rate_matrix=array(count_matrix_3),\
            motif_probs=aa_freqs_3,\
            alphabet=Alphabet(aa_order_3),recode_gaps=True,do_scaling=True,\

src/p/y/pycogent-HEAD/tests/test_evolve/test_coevolution.py   pycogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel, Empirical
from cogent.app.gctmpca import gctmpca_aa_order,\
 default_gctmpca_aa_sub_matrix
        aa_freqs_3 = {'A':0.5,'C':0.3,'D':0.2}
        sm = Empirical(\
            rate_matrix=array(count_matrix_3),\
            motif_probs=aa_freqs_3,\
            alphabet=Alphabet(aa_order_3),recode_gaps=True,do_scaling=True,\