skbio.alignment.Alignment.position_frequencies¶

Alignment.position_frequencies()[source]¶

Return frequencies of characters for positions in Alignment

Returns:	list List of collection.defaultdict objects, one for each position in the Alignment, representing the frequency of each character in the Alignment at that position.

See also

position_counters, position_entropies, k_word_frequencies

Examples

>>> from skbio.alignment import Alignment
>>> from skbio.sequence import DNA
>>> sequences = [DNA('AC--', id="seq1"),
...              DNA('AT-C', id="seq2"),
...              DNA('TT-C', id="seq3")]
>>> a1 = Alignment(sequences)
>>> position_freqs = a1.position_frequencies()
>>> round(position_freqs[0]['A'], 3)
0.667
>>> round(position_freqs[1]['A'], 3)
0.0