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README.md

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2. FASTA file input <br>
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`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --output reports/alignment.txt` <br>
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data/seq1.fasta and data/seq2.fasta each contain exactly one record. <br>
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The text report is saved to reports/alignment.txt <br>
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--> data/seq1.fasta and data/seq2.fasta each contain exactly one record <br>
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--> the text report is saved to /reports <br>
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3. Custom scoring. Override match, mismatch, and gap scores. <br>
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`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --match 2 --mismatch -1 --gap -2`

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