| Program name | Description | 
|---|
| backtranambig | Back translate a protein sequence to ambiguous codons | 
| backtranseq | Back translate a protein sequence | 
| charge | Protein charge plot | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| emowse | Protein identification by mass spectrometry | 
| freak | Residue/base frequency table or plot | 
| iep | Calculates the isoelectric point of a protein | 
| mwcontam | Shows molwts that match across a set of files | 
| mwfilter | Filter noisy molwts from mass spec output | 
| octanol | Displays protein hydropathy | 
| pepinfo | Plots simple amino acid properties in parallel | 
| pepstats | Protein statistics | 
| pepwindow | Displays protein hydropathy | 
| pepwindowall | Displays protein hydropathy of a set of sequences |