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Sourcecode: python-biopython version File versions

Bio::SubsMat Namespace Reference


Detailed Description

Substitution matrices, log odds matrices, and operations on them.


Classes

class  BadMatrix
class  SeqMat

Namespaces

namespace  MatrixInfo

Functions

def _build_exp_freq_mat
def _build_log_odds_mat
def _build_obs_freq_mat
def _build_subs_mat
def _exp_freq_table_from_obs_freq
def make_log_odds_matrix
def observed_frequency_to_substitution_matrix
def read_text_matrix
def two_mat_DJS
 Gives the linear correlation coefficient between two matrices def two_mat_correlation(mat_1, mat_2): Wait for the statistical package before uncommenting this.
def two_mat_relative_entropy

Variables

int ACCREP = 1
tuple BadMatrixError = BadMatrix()
int diagALL = 3
int diagNO = 1
int diagONLY = 2
float EPSILON = 0.00000000000001
int EXPFREQ = 4
int LO = 5
 log = math.log
int NOTYPE = 0
int OBSFREQ = 2
int SUBS = 3


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