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This package implements a Smith-Waterman style local alignment algorithm. You can align a query sequence to a reference. The scoring functions can be based on a matrix, or simple identity. Weights can be adjusted for match/mismatch and gaps, with gap extention penalties. Additionally, the gap penalty can be subject to a decay to prioritize long gaps.

The input files are FASTA format sequences, or strings of sequences.

Here is some skeleton code to get you started:

import swalign
# choose your own values here… 2 and -1 are common.
match = 2
mismatch = -1
scoring = swalign.NucleotideScoringMatrix(match, mismatch)

sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
alignment = sw.align('ACACACTA','AGCACACA')

For other uses, see the script in bin/swalign or