get_pairwise_sequence_identity
#
- biotite.sequence.align.get_pairwise_sequence_identity(alignment, mode='not_terminal')[source]#
Calculate the pairwise sequence identity for an alignment.
The identity is equal to the matches divided by a measure for the length of the alignment that depends on the mode parameter.
- Parameters:
- alignmentAlignment, length=n
The alignment to calculate the pairwise sequence identity for.
- mode{‘all’, ‘not_terminal’, ‘shortest’}, optional
The calculation mode for alignment length.
all - The number of matches divided by the number of all alignment columns.
not_terminal - The number of matches divided by the number of alignment columns that are not terminal gaps in any of the two considered sequences.
shortest - The number of matches divided by the length of the shortest one of the two sequences.
Default is not_terminal.
- Returns:
- identityndarray, dtype=float, shape=(n,n)
The pairwise sequence identity, ranging between 0 and 1.
See also