| Program name | Description | 
|---|
| checktrans | Report STOP codons and ORF statistics of a protein | 
| getorf | Find and extract open reading frames (ORFs) | 
| marscan | Find matrix/scaffold recognition (MRS) signatures in DNA sequences | 
| plotorf | Plot potential open reading frames in a nucleotide sequence | 
| showorf | Display a nucleotide sequence and translation in pretty format | 
| sixpack | Display a DNA sequence with 6-frame translation and ORFs | 
| syco | Draw synonymous codon usage statistic plot for a nucleotide sequence | 
| tcode | Identify protein-coding regions using Fickett TESTCODE statistic | 
| wobble | Plot third base position variability in a nucleotide sequence |