Bio.SubsMat

Package Bio :: Package SubsMat

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Package Bio.SubsMat

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

Submodules
`FreqTable` `MatrixInfo`: A whole bunch of substitution matrices for use in alignments, etc.

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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