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src/c/o/cogent-1.5.3/cogent/evolve/models.py   cogent(Download)
    See Yap, Lindsay, Easteal and Huttley, Mol Biol Evol, In press."""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    See Yap, Lindsay, Easteal and Huttley, Mol Biol Evol, In press."""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    see, Muse and Gaut, 1994, Mol Biol Evol, 11, 715-24"""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    see, Muse and Gaut, 1994, Mol Biol Evol, 11, 715-24"""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
def Y98(**kw):
    """Yang's 1998 substitution model, a derivative of the GY94.
    see Z Yang. Mol. Biol. Evol., 15(5):568-73, 1998"""
    return substitution_model.Codon(
            motif_probs = None,

src/p/y/pycogent-HEAD/cogent/evolve/models.py   pycogent(Download)
    See Yap, Lindsay, Easteal and Huttley, Mol Biol Evol, In press."""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    See Yap, Lindsay, Easteal and Huttley, Mol Biol Evol, In press."""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    see, Muse and Gaut, 1994, Mol Biol Evol, 11, 715-24"""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
    see, Muse and Gaut, 1994, Mol Biol Evol, 11, 715-24"""
    return substitution_model.Codon(
            motif_probs = None,
            do_scaling = True,
            model_gaps = False,
def Y98(**kw):
    """Yang's 1998 substitution model, a derivative of the GY94.
    see Z Yang. Mol. Biol. Evol., 15(5):568-73, 1998"""
    return substitution_model.Codon(
            motif_probs = None,

src/c/o/cogent-1.5.3/tests/test_evolve/test_scale_rules.py   cogent(Download)
    def test_scaling(self):
        """Testing scaling calculations using Dn and Ds as an example."""
        model = substitution_model.Codon(
            do_scaling=True, model_gaps=False, recode_gaps=True,
            predicates = {

src/p/y/pycogent-HEAD/tests/test_evolve/test_scale_rules.py   pycogent(Download)
    def test_scaling(self):
        """Testing scaling calculations using Dn and Ds as an example."""
        model = substitution_model.Codon(
            do_scaling=True, model_gaps=False, recode_gaps=True,
            predicates = {

src/c/o/cogent-1.5.3/tests/test_evolve/test_likelihood_function.py   cogent(Download)
    def test_binned_gamma(self):
        """just rate is gamma distributed"""
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', distribution='gamma', mprob_model='tuple')
    def test_binned_gamma_ordered_param(self):
        """rate is gamma distributed omega follows"""
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', partitioned_params='omega', 
    def test_binned_partition(self):
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', partitioned_params='omega', 
            distribution='free', mprob_model='tuple')
    def test_complex_binned_partition(self):
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='kappa', partitioned_params=['omega'], 
            mprob_model='tuple')
    def test_codon(self):
        """test a three taxa codon model."""
        submod = substitution_model.Codon(
            equal_motif_probs=True,
            do_scaling=False,

src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
    def test_binned_gamma(self):
        """just rate is gamma distributed"""
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', distribution='gamma', mprob_model='tuple')
    def test_binned_gamma_ordered_param(self):
        """rate is gamma distributed omega follows"""
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', partitioned_params='omega', 
    def test_binned_partition(self):
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='rate', partitioned_params='omega', 
            distribution='free', mprob_model='tuple')
    def test_complex_binned_partition(self):
        submod = substitution_model.Codon(
            predicates={'kappa': 'transition', 'omega': 'replacement'},
            ordered_param='kappa', partitioned_params=['omega'], 
            mprob_model='tuple')
    def test_codon(self):
        """test a three taxa codon model."""
        submod = substitution_model.Codon(
            equal_motif_probs=True,
            do_scaling=False,

src/c/o/cogent-1.5.3/tests/test_evolve/test_substitution_model.py   cogent(Download)
    def setUp(self):
        self.standardcode = substitution_model.Codon(model_gaps=True, gc=1,
            mprob_model='tuple')
        self.mitocode = substitution_model.Codon(model_gaps=False, gc=2,
            mprob_model='tuple')

src/p/y/pycogent-HEAD/tests/test_evolve/test_substitution_model.py   pycogent(Download)
    def setUp(self):
        self.standardcode = substitution_model.Codon(model_gaps=True, gc=1,
            mprob_model='tuple')
        self.mitocode = substitution_model.Codon(model_gaps=False, gc=2,
            mprob_model='tuple')

src/c/o/cogent-1.5.3/tests/test_align/test_align.py   cogent(Download)
    def test_codon(self):
        s1 = DNA.makeSequence('tacgccgta', Name="A")
        s2 = DNA.makeSequence('tacgta', Name="B")
        codon_model = cogent.evolve.substitution_model.Codon(
                                 model_gaps=False, equal_motif_probs=True,

src/p/y/pycogent-HEAD/tests/test_align/test_align.py   pycogent(Download)
    def test_codon(self):
        s1 = DNA.makeSequence('tacgccgta', Name="A")
        s2 = DNA.makeSequence('tacgta', Name="B")
        codon_model = cogent.evolve.substitution_model.Codon(
                                 model_gaps=False, equal_motif_probs=True,

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