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src/c/o/cogent-1.5.3/cogent/parse/paml_matrix.py   cogent(Download)
Float = numpy.core.numerictypes.sctype2char(float)
 
from cogent.evolve import substitution_model
 
__author__ = "Matthew Wakefield"

src/c/o/cogent-1.5.3/cogent/evolve/models.py   cogent(Download)
 
import numpy
from cogent.evolve import substitution_model
from cogent.evolve.predicate import MotifChange, replacement
from cogent.evolve.solved_models import F81, HKY85, TN93

src/p/y/pycogent-HEAD/cogent/parse/paml_matrix.py   pycogent(Download)
Float = numpy.core.numerictypes.sctype2char(float)
 
from cogent.evolve import substitution_model
 
__author__ = "Matthew Wakefield"

src/p/y/pycogent-HEAD/cogent/evolve/models.py   pycogent(Download)
 
import numpy
from cogent.evolve import substitution_model
from cogent.evolve.predicate import MotifChange, replacement
from cogent.evolve.solved_models import F81, HKY85, TN93

src/p/y/pycogent-HEAD/tests/test_evolve/test_substitution_model.py   pycogent(Download)
from cogent import LoadSeqs, CodonAlphabet, DNA, LoadTable
from cogent.core import genetic_code
from cogent.evolve import substitution_model, substitution_calculation
from cogent.util.unit_test import TestCase, main
 

src/p/y/pycogent-HEAD/tests/test_evolve/test_simulation.py   pycogent(Download)
import sys
from cogent.core import alignment, tree
from cogent.evolve import substitution_model
 
__author__ = "Peter Maxwell and Gavin Huttley"

src/p/y/pycogent-HEAD/tests/test_evolve/test_scale_rules.py   pycogent(Download)
#!/usr/bin/env python
 
import unittest
from cogent import LoadTree
from cogent.evolve import substitution_model

src/p/y/pycogent-HEAD/tests/test_evolve/test_parameter_controller.py   pycogent(Download)
 
from cogent import LoadSeqs, LoadTree
import cogent.evolve.parameter_controller, cogent.evolve.substitution_model
from cogent.maths import optimisers
 

src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
from numpy import ones, dot
 
from cogent.evolve import substitution_model, predicate
from cogent import DNA, LoadSeqs, LoadTree
from cogent.util.unit_test import TestCase, main

src/p/y/pycogent-HEAD/tests/test_evolve/test_bootstrap.py   pycogent(Download)
import unittest
 
from cogent.evolve import likelihood_function, \
     parameter_controller, substitution_model, bootstrap
 

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