| bestMismatch | Find fewest mismatches |
| combineAligns | Combine gapped alignments |
| complimentDna | Compliment DNA |
| dot-hamming | Wrapper for .C Hamming function |
| hamming | Find hamming distance between many strings |
| leven | Find Levenshtein distance between many strings |
| levenAlign | Align many strings to a reference |
| levenAll | Wrapper for .C Levenshtein function |
| levenR-package | Simple Levenshtein alignments |
| multiMismatch | Find fewest mismatches for multiple patterns |
| revComp | Reverse compliment dna |
| reverseString | Reverse a string |
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