skbio.alignment.multi_align_nucl#

skbio.alignment.multi_align_nucl(sequences, /, **kwargs)[source]#

Align multiple nucleotide sequences.

This is a convenience wrapper of multi_align for nucleotide sequence alignment. It is preloaded with a scoring scheme consistent with BLASTN’s defaults [1]: match score = 2, mismatch score = -3, gap opening penalty = 5, gap extension penalty = 2. All parameters remain customizable. Refer to multi_align for full documentation.

See also

multi_align
multi_align_prot

References

[1]

https://www.ncbi.nlm.nih.gov/books/NBK279684/

Examples

>>> from skbio.sequence import DNA
>>> from skbio.alignment import multi_align_nucl
>>> seqs = [DNA("CAGCTATATATCGCTACG"),
...         DNA("CTGCTTATATCCCTAGG"),
...         DNA("AAGCTATACATCCTTCACG")]
>>> path = multi_align_nucl(seqs).path
>>> for seq in path.to_aligned(seqs):
...     print(seq)
CAGCTATATATCGCT-ACG
CTGCT-TATATCCCT-AGG
AAGCTATACATCCTTCACG