Computes the nucleotide or amino acid frequency at each position in the alignment.
DNAStringSet or AAStringSet with the aligned haplotype sequences.
An optional numeric vector with the haplotype counts.
Matrix with the frequency of each nucleotide or amino acid in each position. A (4 x n) or (20 x n) matrix, where n is the alignment length.
Mercedes Guerrero-Murillo and Josep Gregori
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