| combine.table | Combine Table |
| final.score | Final Score |
| get.context | Get Context |
| get.exprobntcx | get.exprobntcx |
| get.nucleotide.chunk.counts | Get Nucleotide Chunk Counts |
| get.pair | Get Pair |
| get.tn | Get Trinucleotides |
| get.toptn | Get Top Trinucleotides |
| get.trinucleotide.counts | Get Trinucleotide Counts |
| seqkat | SeqKat |
| test.kataegis | Test Kataegis |