Package Bio :: Package SubsMat
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Package Bio.SubsMat

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

Classes
SeqMat A Generic sequence matrix class The key is a 2-tuple containing the letter indices of the matrix.

Exceptions
BadMatrix Exception raised when verifying a matrix

Function Summary
  make_log_odds_matrix(acc_rep_mat, exp_freq_table, logbase, factor, round_digit, keep_nd)
  observed_frequency_to_substitution_matrix(obs_freq_mat)
  read_text_matrix(data_file, mat_type)
  two_mat_DJS(mat_1, mat_2, pi_1, pi_2)
  two_mat_relative_entropy(mat_1, mat_2, logbase, diag)

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