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All Samples(14)  |  Call(12)  |  Derive(0)  |  Import(2)

src/c/o/cogent-1.5.3/cogent/evolve/models.py   cogent(Download)
    Matrix imported from PAML dayhoff.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    DSO78_matrix, DSO78_freqs, name='DSO78', **kw)
 
    return sm
    Matrix imported from PAML jones.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    JTT92_matrix, JTT92_freqs, name='JTT92', **kw)
 
    return sm
    Matrix imported from PAML mtREV24.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    AH96_matrix,
                    AH96_freqs,
                    name='AH96_mtREV24',
    Matrix imported from PAML mtmam.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    AH96_mtmammals_matrix,
                    AH96_mtmammals_freqs,
                    name='AH96_mtmammals',
    Matrix imported from PAML wag.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    WG01_matrix,
                    WG01_freqs,
                    name='WG01',

src/p/y/pycogent-HEAD/cogent/evolve/models.py   pycogent(Download)
    Matrix imported from PAML dayhoff.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    DSO78_matrix, DSO78_freqs, name='DSO78', **kw)
 
    return sm
    Matrix imported from PAML jones.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    JTT92_matrix, JTT92_freqs, name='JTT92', **kw)
 
    return sm
    Matrix imported from PAML mtREV24.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    AH96_matrix,
                    AH96_freqs,
                    name='AH96_mtREV24',
    Matrix imported from PAML mtmam.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    AH96_mtmammals_matrix,
                    AH96_mtmammals_freqs,
                    name='AH96_mtmammals',
    Matrix imported from PAML wag.dat file"""
    sm = substitution_model.EmpiricalProteinMatrix(
                    WG01_matrix,
                    WG01_freqs,
                    name='WG01',

src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
    alphabets, recode_freq_vector, recode_counts_and_freqs, \
    square_matrix_to_dict
from cogent.evolve.substitution_model import EmpiricalProteinMatrix
 
__author__ = "Greg Caporaso"
def build_rate_matrix(count_matrix,freqs,aa_order='ACDEFGHIKLMNPQRSTVWY'):
 
    epm = EmpiricalProteinMatrix(count_matrix,freqs)
    word_probs = array([freqs[aa] for aa in aa_order])
    num = word_probs.shape[0]

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
    alphabets, recode_freq_vector, recode_counts_and_freqs, \
    square_matrix_to_dict
from cogent.evolve.substitution_model import EmpiricalProteinMatrix
 
__author__ = "Greg Caporaso"
def build_rate_matrix(count_matrix,freqs,aa_order='ACDEFGHIKLMNPQRSTVWY'):
 
    epm = EmpiricalProteinMatrix(count_matrix,freqs)
    word_probs = array([freqs[aa] for aa in aa_order])
    num = word_probs.shape[0]