| aaindexextract | Extract amino acid property data from AAINDEX |
| abiview | Display the trace in an ABI sequencer file |
| acdc | Test an application ACD file |
| acdpretty | Correctly reformat an application ACD file |
| acdtable | Generate an HTML table of parameters from an application ACD file |
| acdtrace | Trace processing of an application ACD file (for testing) |
| acdvalid | Validate an application ACD file |
| aligncopy | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| antigenic | Finds antigenic sites in proteins |
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
| backtranseq | Back-translate a protein sequence to a nucleotide sequence |
| banana | Plot bending and curvature data for B-DNA |
| biosed | Replace or delete sequence sections |
| btwisted | Calculate the twisting in a B-DNA sequence |
| cai | Calculate codon adaptation index |
| chaos | Draw a chaos game representation plot for a nucleotide sequence |
| charge | Draw a protein charge plot |
| checktrans | Reports STOP codons and ORF statistics of a protein |
| chips | Calculates Nc codon usage statistic |
| cirdna | Draws circular maps of DNA constructs |
| codcmp | Codon usage table comparison |
| codcopy | Copy and reformat a codon usage table |
| coderet | Extract CDS, mRNA and translations from feature tables |
| compseq | Calculate the composition of unique words in sequences |
| cons | Create a consensus sequence from a multiple alignment |
| consambig | Create an ambiguous consensus sequence from a multiple alignment |
| cpgplot | Identify and plot CpG islands in nucleotide sequence(s) |
| cpgreport | Identify and report CpG-rich regions in nucleotide sequence(s) |
| cusp | Create a codon usage table from nucleotide sequence(s) |
| cutgextract | Extract codon usage tables from CUTG database |
| cutseq | Removes a section from a sequence |
| dan | Calculates nucleic acid melting temperature |
| dbiblast | Index a BLAST database |
| dbifasta | Index a fasta file database |
| dbiflat | Index a flat file database |
| dbigcg | Index a GCG formatted database |
| dbxfasta | Index a fasta file database using b+tree indices |
| dbxflat | Index a flat file database using b+tree indices |
| dbxgcg | Index a GCG formatted database using b+tree indices |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| density | Draw a nucleic acid density plot |
| descseq | Alter the name or description of a sequence |
| diffseq | Compare and report features of two similar sequences |
| digest | Reports on protein proteolytic enzyme or reagent cleavage sites |
| distmat | Create a distance matrix from a multiple sequence alignment |
| dotmatcher | Draw a threshold dotplot of two sequences |
| dotpath | Draw a non-overlapping wordmatch dotplot of two sequences |
| dottup | Displays a wordmatch dotplot of two sequences |
| dreg | Regular expression search of nucleotide sequence(s) |
| edialign | Local multiple alignment of sequences |
| einverted | Finds inverted repeats in nucleotide sequences |
| embossdata | Find and retrieve EMBOSS data files |
| embossversion | Reports the current EMBOSS version number |
| emma | Multiple sequence alignment (ClustalW wrapper) |
| emowse | Search protein sequences by digest fragment molecular weight |
| entret | Retrieves sequence entries from flatfile databases and files |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| eprimer3 | Picks PCR primers and hybridization oligos |
| equicktandem | Finds tandem repeats in nucleotide sequences |
| est2genome | Align EST sequences to genomic DNA sequence |
| etandem | Finds tandem repeats in a nucleotide sequence |
| extractalign | Extract regions from a sequence alignment |
| extractfeat | Extract features from sequence(s) |
| extractseq | Extract regions from a sequence |
| featcopy | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| findkm | Calculate and plot enzyme reaction data |
| freak | Generate residue/base frequency table or plot |
| fuzznuc | Search for patterns in nucleotide sequences |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| garnier | Predicts protein secondary structure using GOR method |
| geecee | Calculate fractional GC content of nucleic acid sequences |
| getorf | Finds and extracts open reading frames (ORFs) |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| hmoment | Calculate and plot hydrophobic moment for protein sequence(s) |
| iep | Calculate the isoelectric point of proteins |
| infoalign | Display basic information about a multiple sequence alignment |
| infobase | Return information on a given nucleotide base |
| inforesidue | Return information on a given amino acid residue |
| infoseq | Display basic information about sequences |
| isochore | Plots isochores in DNA sequences |
| jaspextract | Extract data from JASPAR |
| jaspscan | Scans DNA sequences for transcription factors |
| lindna | Draws linear maps of DNA constructs |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Create random nucleotide sequences |
| makeprotseq | Create random protein sequences |
| marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
| maskambignuc | Masks all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Masks all ambiguity characters in protein sequences with X |
| maskfeat | Write a sequence with masked features |
| maskseq | Write a sequence with masked regions |
| matcher | Waterman-Eggert local alignment of two sequences |
| megamerger | Merge two large overlapping DNA sequences |
| merger | Merge two overlapping sequences |
| msbar | Mutate a sequence |
| mwcontam | Find weights common to multiple molecular weights files |
| mwfilter | Filter noisy data from molecular weights file |
| needle | Needleman-Wunsch global alignment of two sequences |
| needleall | Many-to-many pairwise alignments of two sequence sets |
| newcpgreport | Identify CpG islands in nucleotide sequence(s) |
| newcpgseek | Identify and report CpG-rich regions in nucleotide sequence(s) |
| newseq | Create a sequence file from a typed-in sequence |
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
| noreturn | Remove carriage return from ASCII files |
| nospace | Remove all whitespace from an ASCII text file |
| notab | Replace tabs with spaces in an ASCII text file |
| notseq | Write to file a subset of an input stream of sequences |
| nthseq | Write to file a single sequence from an input stream of sequences |
| nthseqset | Reads and writes (returns) one set of sequences from many |
| octanol | Draw a White-Wimley protein hydropathy plot |
| oddcomp | Identify proteins with specified sequence word composition |
| palindrome | Finds inverted repeats in nucleotide sequence(s) |
| pasteseq | Insert one sequence into another |
| patmatdb | Searches protein sequences with a sequence motif |
| patmatmotifs | Scan a protein sequence with motifs from the PROSITE database |
| pepcoil | Predicts coiled coil regions in protein sequences |
| pepinfo | Plot amino acid properties of a protein sequence in parallel |
| pepnet | Draw a helical net for a protein sequence |
| pepstats | Calculates statistics of protein properties |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| pepwindow | Draw a hydropathy plot for a protein sequence |
| pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment |
| plotcon | Plot conservation of a sequence alignment |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| polydot | Draw dotplots for all-against-all comparison of a sequence set |
| preg | Regular expression search of protein sequence(s) |
| prettyplot | Draw a sequence alignment with pretty formatting |
| prettyseq | Write a nucleotide sequence and its translation to file |
| primersearch | Search DNA sequences for matches with primer pairs |
| printsextract | Extract data from PRINTS database for use by pscan |
| profit | Scan one or more sequences with a simple frequency matrix |
| prophecy | Create frequency matrix or profile from a multiple alignment |
| prophet | Scan one or more sequences with a Gribskov or Henikoff profile |
| prosextract | Processes the PROSITE motif database for use by patmatmotifs |
| pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| recoder | Find restriction sites to remove (mutate) with no translation change |
| redata | Retrieve information from REBASE restriction enzyme database |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| restover | Find restriction enzymes producing a specific overhang |
| restrict | Report restriction enzyme cleavage sites in a nucleotide sequence |
| revseq | Reverse and complement a nucleotide sequence |
| seealso | Finds programs with similar function to a specified program |
| seqmatchall | All-against-all word comparison of a sequence set |
| seqret | Reads and writes (returns) sequences |
| seqretsetall | Reads and writes (returns) many sets of sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| showalign | Display a multiple sequence alignment in pretty format |
| showdb | Displays information on configured databases |
| showfeat | Display features of a sequence in pretty format |
| showorf | Display a nucleotide sequence and translation in pretty format |
| showpep | Displays protein sequences with features in pretty format |
| showseq | Displays sequences with features in pretty format |
| shuffleseq | Shuffles a set of sequences maintaining composition |
| sigcleave | Reports on signal cleavage sites in a protein sequence |
| silent | Find restriction sites to insert (mutate) with no translation change |
| sirna | Finds siRNA duplexes in mRNA |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitsource | Split sequence(s) into original source sequences |
| splitter | Split sequence(s) into smaller sequences |
| stretcher | Needleman-Wunsch rapid global alignment of two sequences |
| stssearch | Search a DNA database for matches with a set of STS primers |
| supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
| syco | Draw synonymous codon usage statistic plot for a nucleotide sequence |
| tcode | Identify protein-coding regions using Fickett TESTCODE statistic |
| textsearch | Search the textual description of sequence(s) |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |
| tfm | Displays full documentation for an application |
| tfscan | Identify transcription factor binding sites in DNA sequences |
| tmap | Predict and plot transmembrane segments in protein sequences |
| tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
| transeq | Translate nucleic acid sequences |
| trimest | Remove poly-A tails from nucleotide sequences |
| trimseq | Remove unwanted characters from start and end of sequence(s) |
| trimspace | Remove extra whitespace from an ASCII text file |
| twofeat | Finds neighbouring pairs of features in sequence(s) |
| union | Concatenate multiple sequences into a single sequence |
| vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
| water | Smith-Waterman local alignment of sequences |
| whichdb | Search all sequence databases for an entry and retrieve it |
| wobble | Plot third base position variability in a nucleotide sequence |
| wordcount | Count and extract unique words in molecular sequence(s) |
| wordfinder | Match large sequences against one or more other sequences |
| wordmatch | Finds regions of identity (exact matches) of two sequences |
| wossname | Finds programs by keywords in their short description |
| yank | Add a sequence reference (a full USA) to a list file |