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Simple Python Implementation of the Smith-Waterman and Needleman-Wunsch Algorithms
pip install EasyAlign==0.1
Thanks for using EasyAlign! :) You can install with pip! pip install EasyAlign This software can align python lists of any objects that can be compared with the '==' operator (including strings!) To use it from EasyAlign import LocalAligner, GlobalAligner seq1 = [5, 1, 2, 3, 4, 5] seq2 = [5, 1, 1, 1, 1, 1, 2, 3] my_local_aligner = LocalAligner(2, -1) aligned_seq1, aligned_seq2, score = my_local_aligner.align(seq1, seq2) print(aligned_seq1, aligned_seq2, score ) my_global_aligner = GlobalAligner(2, -1) aligned_seq1, aligned_seq2, score = my_global_aligner.align(seq1, seq2) print(aligned_seq1, aligned_seq2, score ) If you want to look at more local alignments than just the best scored one you can directly access the score table from the last alignment using my_local_aligner.table - it's a 2d list of integers. You can then pass the x,y coordinates (seq1 is x, seq2 is y) to my_local_aligner.traceback(x,y) which will return the aligned local sequences that end at that x/y coord.
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Last synced: 2021-02-14 23:33:41 UTC
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