cocoatree.statistics.pairwise.compute_sca_matrix¶

cocoatree.statistics.pairwise.compute_sca_matrix(sequences, seq_weights=None, raw_correlation=False, freq_regul=0.03)[source]¶

Compute the SCA coevolution matrix

\[C_{ij}^{ab} = f_{ij}^{ab} - f_i^a f_j^b\]

\[\tilde{C_{ij}} = \sqrt{sum_{a,b} \tilde{(C_{ij}^{ab})^2}}\]

Parameters¶

sequences : list of sequences

seq_weightsndarray (nseq), optional, default: None: if None, will compute sequence weights
raw_correlationboolean, optional, default: False: whether to return raw correlations

freq_regul : regularization parameter (default=__freq_regularization_ref)

SCA_matrix : SCA coevolution matrix