| Application | Description |
|---|---|
| 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 |
| Application | Description |
|---|---|
| cons | Create a consensus sequence from a multiple alignment |
| consambig | Create an ambiguous consensus sequence from a multiple alignment |
| megamerger | Merge two large overlapping DNA sequences |
| merger | Merge two overlapping sequences |
| Application | Description |
|---|---|
| diffseq | Compare and report features of two similar sequences |
| Application | Description |
|---|---|
| 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 |
| polydot | Draw dotplots for all-against-all comparison of a sequence set |
| Application | Description |
|---|---|
| est2genome | Align EST sequences to genomic DNA sequence |
| needle | Needleman-Wunsch global alignment of two sequences |
| needleall | Many-to-many pairwise alignments of two sequence sets |
| stretcher | Needleman-Wunsch rapid global alignment of two sequences |
| Application | Description |
|---|---|
| matcher | Waterman-Eggert local alignment of two sequences |
| seqmatchall | All-against-all word comparison of a sequence set |
| supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
| water | Smith-Waterman local alignment of sequences |
| wordfinder | Match large sequences against one or more other sequences |
| wordmatch | Finds regions of identity (exact matches) of two sequences |
| Application | Description |
|---|---|
| edialign | Local multiple alignment of sequences |
| emma | Multiple sequence alignment (ClustalW wrapper) |
| infoalign | Display basic information about a multiple sequence alignment |
| plotcon | Plot conservation of a sequence alignment |
| prettyplot | Draw a sequence alignment with pretty formatting |
| showalign | Display a multiple sequence alignment in pretty format |
| tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
| Application | Description |
|---|---|
| abiview | Display the trace in an ABI sequencer file |
| cirdna | Draws circular maps of DNA constructs |
| lindna | Draws linear maps of DNA constructs |
| pepnet | Draw a helical net for a protein sequence |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| prettyplot | Draw a sequence alignment with pretty formatting |
| prettyseq | Write a nucleotide sequence and its translation to file |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| seealso | Finds programs with similar function to a specified program |
| showalign | Display a multiple sequence alignment in pretty format |
| showdb | Displays information on configured databases |
| showfeat | Display features of a sequence in pretty format |
| showpep | Displays protein sequences with features in pretty format |
| showseq | Displays sequences with features in pretty format |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| textsearch | Search the textual description of sequence(s) |
| Application | Description |
|---|---|
| aligncopy | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Removes a section from a sequence |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieves sequence entries from flatfile databases and files |
| 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 |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Create random nucleotide sequences |
| makeprotseq | Create random protein 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 |
| 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 |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsetall | Reads and writes (returns) many sets of sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| 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 |
| 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 |
| union | Concatenate multiple sequences into a single sequence |
| vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |
| Application | Description |
|---|---|
| findkm | Calculate and plot enzyme reaction data |
| Application | Description |
|---|---|
| coderet | Extract CDS, mRNA and translations from feature tables |
| extractfeat | Extract features from sequence(s) |
| maskfeat | Write a sequence with masked features |
| showfeat | Display features of a sequence in pretty format |
| twofeat | Finds neighbouring pairs of features in sequence(s) |
| Application | Description |
|---|---|
| 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 |
| seealso | Finds programs with similar function to a specified program |
| showdb | Displays information on configured databases |
| textsearch | Search the textual description of sequence(s) |
| tfm | Displays full documentation for an application |
| whichdb | Search all sequence databases for an entry and retrieve it |
| wossname | Finds programs by keywords in their short description |
| Application | Description |
|---|---|
| einverted | Finds inverted repeats in nucleotide sequences |
| Application | Description |
|---|---|
| cai | Calculate codon adaptation index |
| chips | Calculates Nc codon usage statistic |
| codcmp | Codon usage table comparison |
| cusp | Create a codon usage table from nucleotide sequence(s) |
| syco | Draw synonymous codon usage statistic plot for a nucleotide sequence |
| Application | Description |
|---|---|
| banana | Plot bending and curvature data for B-DNA |
| btwisted | Calculate the twisting in a B-DNA sequence |
| chaos | Draw a chaos game representation plot for a nucleotide sequence |
| compseq | Calculate the composition of unique words in sequences |
| dan | Calculates nucleic acid melting temperature |
| density | Draw a nucleic acid density plot |
| freak | Generate residue/base frequency table or plot |
| isochore | Plots isochores in DNA sequences |
| sirna | Finds siRNA duplexes in mRNA |
| wordcount | Count and extract unique words in molecular sequence(s) |
| Application | Description |
|---|---|
| cpgplot | Identify and plot CpG islands in nucleotide sequence(s) |
| cpgreport | Identify and report CpG-rich regions in nucleotide sequence(s) |
| geecee | Calculate fractional GC content of nucleic acid sequences |
| newcpgreport | Identify CpG islands in nucleotide sequence(s) |
| newcpgseek | Identify and report CpG-rich regions in nucleotide sequence(s) |
| Application | Description |
|---|---|
| getorf | Finds and extracts open reading frames (ORFs) |
| marscan | Finds 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 |
| Application | Description |
|---|---|
| dreg | Regular expression search of nucleotide sequence(s) |
| fuzznuc | Search for patterns in nucleotide sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
| Application | Description |
|---|---|
| msbar | Mutate a sequence |
| shuffleseq | Shuffles a set of sequences maintaining composition |
| Application | Description |
|---|---|
| eprimer3 | Picks PCR primers and hybridization oligos |
| primersearch | Search DNA sequences for matches with primer pairs |
| stssearch | Search a DNA database for matches with a set of STS primers |
| Application | Description |
|---|---|
| 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 |
| Application | Description |
|---|---|
| einverted | Finds inverted repeats in nucleotide sequences |
| equicktandem | Finds tandem repeats in nucleotide sequences |
| etandem | Finds tandem repeats in a nucleotide sequence |
| palindrome | Finds inverted repeats in nucleotide sequence(s) |
| Application | Description |
|---|---|
| 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 |
| showseq | Displays sequences with features in pretty format |
| silent | Find restriction sites to insert (mutate) with no translation change |
| Application | Description |
|---|---|
| jaspscan | Scans DNA sequences for transcription factors |
| tfscan | Identify transcription factor binding sites in DNA sequences |
| Application | Description |
|---|---|
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
| backtranseq | Back-translate a protein sequence to a nucleotide sequence |
| coderet | Extract CDS, mRNA and translations from feature tables |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| prettyseq | Write a nucleotide sequence and its translation to file |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| showorf | Display a nucleotide sequence and translation in pretty format |
| showseq | Displays sequences with features in pretty format |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| transeq | Translate nucleic acid sequences |
| Application | Description |
|---|---|
| distmat | Create a distance matrix from a multiple sequence alignment |
| Application | Description |
|---|---|
| garnier | Predicts protein secondary structure using GOR method |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| hmoment | Calculate and plot hydrophobic moment for protein sequence(s) |
| pepcoil | Predicts coiled coil regions in protein sequences |
| pepnet | Draw a helical net for a protein sequence |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| tmap | Predict and plot transmembrane segments in protein sequences |
| Application | Description |
|---|---|
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| Application | Description |
|---|---|
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
| backtranseq | Back-translate a protein sequence to a nucleotide sequence |
| charge | Draw a protein charge plot |
| checktrans | Reports STOP codons and ORF statistics of a protein |
| compseq | Calculate the composition of unique words in sequences |
| emowse | Search protein sequences by digest fragment molecular weight |
| freak | Generate residue/base frequency table or plot |
| iep | Calculate the isoelectric point of proteins |
| mwcontam | Find weights common to multiple molecular weights files |
| mwfilter | Filter noisy data from molecular weights file |
| octanol | Draw a White-Wimley protein hydropathy plot |
| pepinfo | Plot amino acid properties of a protein sequence in parallel |
| pepstats | Calculates statistics of protein properties |
| pepwindow | Draw a hydropathy plot for a protein sequence |
| pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment |
| wordcount | Count and extract unique words in molecular sequence(s) |
| Application | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| digest | Reports on protein proteolytic enzyme or reagent cleavage sites |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| oddcomp | Identify proteins with specified sequence word composition |
| 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 |
| preg | Regular expression search of protein sequence(s) |
| pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
| sigcleave | Reports on signal cleavage sites in a protein sequence |
| Application | Description |
|---|---|
| msbar | Mutate a sequence |
| shuffleseq | Shuffles a set of sequences maintaining composition |
| Application | Description |
|---|---|
| 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 |
| Application | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| cutgextract | Extract codon usage tables from CUTG database |
| jaspextract | Extract data from JASPAR |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Processes the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |
| Application | Description |
|---|---|
| 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 |
| Application | Description |
|---|---|
| embossdata | Find and retrieve EMBOSS data files |
| embossversion | Reports the current EMBOSS version number |
| Application | Description |
|---|---|
| efitch | Fitch-Margoliash and Least-Squares Distance Methods |
| ekitsch | Fitch-Margoliash method with contemporary tips |
| eneighbor | Phylogenies from distance matrix by N-J or UPGMA method |
| ffitch | Fitch-Margoliash and Least-Squares Distance Methods |
| fkitsch | Fitch-Margoliash method with contemporary tips |
| fneighbor | Phylogenies from distance matrix by N-J or UPGMA method |
| Application | Description |
|---|---|
| oalistat | Statistics for multiple alignment files |
| ohmmalign | Align sequences with an HMM |
| ohmmbuild | Build HMM |
| ohmmcalibrate | Calibrate a hidden Markov model |
| ohmmconvert | Convert between HMM formats |
| ohmmemit | Extract HMM sequences |
| ohmmfetch | Extract HMM from a database |
| ohmmindex | Index an HMM database |
| ohmmpfam | Align single sequence with an HMM |
| ohmmsearch | Search sequence database with an HMM |
| ehmmalign | Align sequences to an HMM profile |
| ehmmbuild | Build a profile HMM from an alignment |
| ehmmcalibrate | Calibrate HMM search statistics |
| ehmmconvert | Convert between profile HMM file formats |
| ehmmemit | Generate sequences from a profile HMM |
| ehmmfetch | Retrieve an HMM from an HMM database |
| ehmmindex | Create a binary SSI index for an HMM database |
| ehmmpfam | Search one or more sequences against an HMM database |
| ehmmsearch | Search a sequence database with a profile HMM |
| Application | Description |
|---|---|
| vrnaalifold | RNA alignment folding |
| vrnaalifoldpf | RNA alignment folding with partition |
| vrnacofold | RNA cofolding |
| vrnacofoldconc | RNA cofolding with concentrations |
| vrnacofoldpf | RNA cofolding with partitioning |
| vrnadistance | RNA distances |
| vrnaduplex | RNA duplex calculation |
| vrnaeval | RNA eval |
| vrnaevalpair | RNA eval with cofold |
| vrnafold | Calculate secondary structures of RNAs |
| vrnafoldpf | Secondary structures of RNAs with partition |
| vrnaheat | RNA melting |
| vrnainverse | RNA sequences matching a structure |
| vrnalfold | Calculate locally stable secondary structures of RNAs |
| vrnaplot | Plot vrnafold output |
| vrnasubopt | Calculate RNA suboptimals |
| Application | Description |
|---|---|
| eclique | Largest clique program |
| edollop | Dollo and polymorphism parsimony algorithm |
| edolpenny | Penny algorithm Dollo or polymorphism |
| efactor | Multistate to binary recoding program |
| emix | Mixed parsimony algorithm |
| epenny | Penny algorithm, branch-and-bound |
| fclique | Largest clique program |
| fdollop | Dollo and polymorphism parsimony algorithm |
| fdolpenny | Penny algorithm Dollo or polymorphism |
| ffactor | Multistate to binary recoding program |
| fmix | Mixed parsimony algorithm |
| fmove | Interactive mixed method parsimony |
| fpars | Discrete character parsimony |
| fpenny | Penny algorithm, branch-and-bound |
| Application | Description |
|---|---|
| fdrawgram | Plots a cladogram- or phenogram-like rooted tree diagram |
| fdrawtree | Plots an unrooted tree diagram |
| fretree | Interactive tree rearrangement |
| Application | Description |
|---|---|
| emnu | Simple menu of EMBOSS applications |
| Application | Description |
|---|---|
| crystalball | Answers every drug discovery question about a sequence |
| myseq | Demonstration of sequence reading |
| mytest | Demonstration of sequence reading |
| Application | Description |
|---|---|
| econtml | Continuous character Maximum Likelihood method |
| econtrast | Continuous character Contrasts |
| fcontrast | Continuous character Contrasts |
| Application | Description |
|---|---|
| tfscan | Scans DNA sequences for transcription factors |
| Application | Description |
|---|---|
| egendist | Genetic Distance Matrix program |
| fcontml | Gene frequency and continuous character Maximum Likelihood |
| fgendist | Compute genetic distances from gene frequencies |
| Application | Description |
|---|---|
| econsense | Majority-rule and strict consensus tree |
| fconsense | Majority-rule and strict consensus tree |
| ftreedist | Distances between trees |
| ftreedistpair | Distances between two sets of trees |