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src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
from cogent.evolve.substitution_model import SubstitutionModel
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA
from cogent.core.tree import TreeError
         not perfectly clear about it.
    """
    sm = sm or SubstitutionModel(aln.Alphabet, recode_gaps=True)
    lf = sm.makeLikelihoodFunction(tree,sm.motif_probs)
    lf.setAlignment(aln, motif_pseudocount=pseudocount)

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
from cogent.evolve.substitution_model import SubstitutionModel
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA
from cogent.core.tree import TreeError
         not perfectly clear about it.
    """
    sm = sm or SubstitutionModel(aln.Alphabet, recode_gaps=True)
    lf = sm.makeLikelihoodFunction(tree,sm.motif_probs)
    lf.setAlignment(aln, motif_pseudocount=pseudocount)

src/p/y/pycogent-HEAD/tests/test_util/test_recode_alignment.py   pycogent(Download)
from cogent.core.alignment import DenseAlignment
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel
from cogent.core.alphabet import Alphabet 
from cogent.app.gctmpca import gctmpca_aa_order,\

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

src/c/o/cogent-1.5.3/tests/test_util/test_recode_alignment.py   cogent(Download)
from cogent.core.alignment import DenseAlignment
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel
from cogent.core.alphabet import Alphabet 
from cogent.app.gctmpca import gctmpca_aa_order,\

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