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| clustalw | Multiple Sequence Alignment |
| complement.DNA | Find the Complement of a DNA/RNA Sequence |
| dna | Procedures for Analysis of DNA Sequences |
| DNAtoProt | Translate Coding DNA/RNA Base Triplets to Amino Acids |
| dotmatrix | Plot a Dot Matrix Comparing Two DNA Sequences |
| find.DNA | Search for Specific Sets of Codes in a DNA Sequence |
| flip | Find Open Reading Frames in a DNA Sequence |
| match.DNA | Find Matches of a Set of Bases in a DNA/RNA Sequence |
| mutations | Calculate Frequencies of Mutation in a Set of Sequences |
| plotCG | Plot the Proportion of C+G along a DNA Sequence |
| read.DNA | Read DNA Sequences from a File in Standard Format |
| stats.DNA | Calculate Descriptive Statistics for a Coding Sequence |