| boxshade | Boxshade: Shading Multiple Aligned Sequences |
| c2s | Convenience Functions to Convert Strings to Character Vectors |
| clustal | Run Multiple Sequence Alignment (ClustalW) on a Set of... |
| dist | Calculate Distances between Sets of Sequences |
| kalign | Multiple Sequence Alignment (Kalign) |
| mafft | Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences |
| MUSCLE | Run Multiple Sequence Alignment (MUSCLE) on a Set of... |
| mutations | Creates Random Mutations of a Sequence |
| plot | Plot Genetic Sequences and Alignments |
| random_sequences | Create a Set of Random Sequences |
| simRank | Compute the SimRank Similarity between Sets of Sequences |
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