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src/c/o/cogent-1.5.3/cogent/evolve/likelihood_function.py   cogent(Download)
from cogent.core.alignment import Alignment
from cogent.util.dict_array import DictArrayTemplate
from cogent.evolve.simulate import AlignmentEvolver, randomSequence
from cogent.util import parallel, table
from cogent.recalculation.definition import ParameterController
            site_bins = numpy.zeros([sequence_length], int)
 
        evolver = AlignmentEvolver(random_series, orig_ambig, exclude_internal,
                self.bin_names, site_bins, psub_for, self._motifs)
 
                random_series, mprobs, sequence_length)
 
        simulated_sequences = evolver(self._tree, root_sequence)
 
        return Alignment(

src/p/y/pycogent-HEAD/cogent/evolve/likelihood_function.py   pycogent(Download)
from cogent.core.alignment import Alignment
from cogent.util.dict_array import DictArrayTemplate
from cogent.evolve.simulate import AlignmentEvolver, randomSequence
from cogent.util import parallel, table
from cogent.recalculation.definition import ParameterController
            site_bins = numpy.zeros([sequence_length], int)
 
        evolver = AlignmentEvolver(random_series, orig_ambig, exclude_internal,
                self.bin_names, site_bins, psub_for, self._motifs)
 
                random_series, mprobs, sequence_length)
 
        simulated_sequences = evolver(self._tree, root_sequence)
 
        return Alignment(