Positional conservation and gap filtering.
Mask (i.e., filter) unconserved and highly gapped columns from an
alignment. Default min_conservation was chosen to reproduce the mask
presented in Lane (1991).
Parameters
- alignment : FeatureData[AlignedSequence]
- The alignment to be masked.
- max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
- The maximum relative frequency of gap characters in a column for the
column to be retained. This relative frequency must be a number between
0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
gap characters, and 1.0 retains all columns regardless of gap character
frequency.
- min_conservation : Float % Range(0, 1, inclusive_end=True), optional
- The minimum relative frequency of at least one non-gap character in a
column for that column to be retained. This relative frequency must be
a number between 0.0 and 1.0 (inclusive). For example, if a value of
0.4 is provided, a column will only be retained if it contains at least
one character that is present in at least 40% of the sequences.
Returns
- masked_alignment : FeatureData[AlignedSequence]
- The masked alignment.