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Python interface for the seq-align C library, written by Isaac Turner (@noporpoise).


pip install pyseq-align

To install directly from GitHub,

git clone --recursive
cd pyseq-align
pip install .


Two alignment algorithms are provided: Needleman-Wunsch and Smith-Waterman.

from pyseq_align import NeedlemanWunsch

nw = NeedlemanWunsch()
al = nw.align('ACGT', 'ACGTC')
print(al.result_a)  # ACGT-
print(al.result_b)  # ACGTC
from pyseq_align import SmithWaterman

sw = SmithWaterman()
als = sw.align('ACGT', 'ACGTC')  # unlike above, this is a list of Alignment's
for al in als:
    print(al.result_a, al.pos_a)  # ACGT, 0
    print(al.result_b, al.pos_b)  # ACGT, 0

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