GitHub - madisonlondon/Nucleotide-Alignment: This program determines the optimal alignment of two nucleotide sequences using the Smith–Waterman algorithm. Optimality, of course, is determined by the values of the gap penalty g and the weight matrix (that lists all of the s(ai , bj )). Finally the program outputs the optimal similarity score along with the optimal alignment.

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Name		Name	Last commit message	Last commit date
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AlignmentMatrixScores.java		AlignmentMatrixScores.java
README		README
SmithWatermanSequenceComparison.java		SmithWatermanSequenceComparison.java

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This code was created by Madison London and Sophie Borchart

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This program determines the optimal alignment of two nucleotide sequences using the Smith–Waterman algorithm. Optimality, of course, is determined by the values of the gap penalty g and the weight matrix (that lists all of the s(ai , bj )). Finally the program outputs the optimal similarity score along with the optimal alignment.

nucleotide-alignment nucleotide-sequence smith-waterman smith-waterman-alignment

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