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python-biopython  1.60
Classes | Namespaces | Functions | Variables
__init__.py File Reference

Go to the source code of this file.

Classes

class  Bio.SubsMat.SeqMat
class  Bio.SubsMat.AcceptedReplacementsMatrix
class  Bio.SubsMat.ObservedFrequencyMatrix
class  Bio.SubsMat.ExpectedFrequencyMatrix
class  Bio.SubsMat.SubstitutionMatrix
class  Bio.SubsMat.LogOddsMatrix

Namespaces

namespace  Bio.SubsMat

Functions

def Bio.SubsMat._build_obs_freq_mat
def Bio.SubsMat._exp_freq_table_from_obs_freq
def Bio.SubsMat._build_exp_freq_mat
def Bio.SubsMat._build_subs_mat
def Bio.SubsMat._build_log_odds_mat
def Bio.SubsMat.make_log_odds_matrix
def Bio.SubsMat.observed_frequency_to_substitution_matrix
def Bio.SubsMat.read_text_matrix
def Bio.SubsMat.two_mat_relative_entropy
def Bio.SubsMat.two_mat_correlation
 Gives the linear correlation coefficient between two matrices.
def Bio.SubsMat.two_mat_DJS

Variables

 Bio.SubsMat.log = math.log
int Bio.SubsMat.NOTYPE = 0
int Bio.SubsMat.ACCREP = 1
int Bio.SubsMat.OBSFREQ = 2
int Bio.SubsMat.SUBS = 3
int Bio.SubsMat.EXPFREQ = 4
int Bio.SubsMat.LO = 5
float Bio.SubsMat.EPSILON = 0.00000000000001
int Bio.SubsMat.diagNO = 1
int Bio.SubsMat.diagONLY = 2
int Bio.SubsMat.diagALL = 3