| tfm

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Displays full documentation for an application

## Description

tfm displays help information for the specified EMBOSS program.

## Usage

Here is a sample session with tfm

##

##

##

    % tfm wossname
    Displays full documentation for an application

    ::::::::::::::
    /homes/pmr/local/share/EMBOSS/doc/programs/text/wossname.txt
    ::::::::::::::
                                      wossname

    Wiki

       The master copies of EMBOSS documentation are available at
       http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

       Please help by correcting and extending the Wiki pages.

    Function

       Finds programs by keywords in their short description

    Description

       wossname search for the specified keywords (or parts thereof) in the
       application short description (as displayed by a program when it
       starts), functional group name and keywords. The group name,
       application name and short description of any matching applications is
       output (screen by default). If no search words are specified, then
       details of all the EMBOSS programs are output. There are various
       options for controlling how the search is performed and what is given
       in the output file. Optionally, the output will be wrapped in HTML tags
       ready for inclusion in a Web page.

    Usage

       Here is a sample session with wossname

       Search for programs with 'restrict' in their description:

    % wossname restrict
    Finds programs by keywords in their short description

    SEARCH FOR 'RESTRICT'
    erestml       Restriction site Maximum Likelihood method
    frestboot     Bootstrapped restriction sites algorithm
    frestdist     Distance matrix from restriction sites or fragments
    frestml       Restriction site maximum Likelihood method
    rebaseextract Process the REBASE database for use by restriction enzyme applicat
    ions
    recoder       Find restriction sites to remove (mutate) with no translation chan
    ge
    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 chan
    ge

       Example 2

       Display a listing of programs in their groups:

    % wossname -search ''
    Finds programs by keywords in their short description

    ACD
    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

    ALIGNMENT CONSENSUS
    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

    ALIGNMENT DIFFERENCES
    diffseq Compare and report features of two similar sequences

    ALIGNMENT DOT PLOTS
    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

    ALIGNMENT GLOBAL
    esim4      Align an mRNA to a genomic DNA sequence
    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

    ALIGNMENT LOCAL
    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 sequence
    s
    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

    ALIGNMENT MULTIPLE
    edialign   Local multiple alignment of sequences
    emma       Multiple sequence alignment (ClustalW wrapper)
    infoalign  Display basic information about a multiple sequence alignment
    mse        Multiple Sequence Editor
    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

    ASSEMBLY FRAGMENT ASSEMBLY
    emira    MIRA fragment assembly program
    emiraest MIRAest fragment assembly program

    DISPLAY
    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)

    EDIT
    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

    ENZYME KINETICS
    findkm Calculate and plot enzyme reaction data

    FEATURE TABLES
    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)

    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
    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

    INFORMATION
    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

    MENUS
    emnu   Simple menu of EMBOSS applications

    NUCLEIC 2D STRUCTURE
    einverted      Finds inverted repeats in nucleotide sequences
    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

    NUCLEIC CODON USAGE
    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

    NUCLEIC COMPOSITION
    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)

    NUCLEIC CPG ISLANDS
    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)

    NUCLEIC GENE FINDING
    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

    NUCLEIC MOTIFS
    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

    NUCLEIC MUTATION
    msbar      Mutate a sequence
    shuffleseq Shuffles a set of sequences maintaining composition

    NUCLEIC PRIMERS
    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

    NUCLEIC PROFILES
    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

    NUCLEIC REPEATS
    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)

    NUCLEIC RESTRICTION
    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

    NUCLEIC RNA FOLDING
    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

    NUCLEIC TRANSCRIPTION
    jaspscan Scans DNA sequences for transcription factors
    tfscan   Identify transcription factor binding sites in DNA sequences

    NUCLEIC TRANSLATION
    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

    PHYLOGENY CONSENSUS
    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

    PHYLOGENY CONTINUOUS CHARACTERS
    econtml   Continuous character Maximum Likelihood method
    econtrast Continuous character Contrasts
    fcontrast Continuous character Contrasts

    PHYLOGENY DISCRETE CHARACTERS
    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

    PHYLOGENY DISTANCE MATRIX
    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

    PHYLOGENY GENE FREQUENCIES
    egendist Genetic Distance Matrix program
    fcontml  Gene frequency and continuous character Maximum Likelihood
    fgendist Compute genetic distances from gene frequencies

    PHYLOGENY MOLECULAR SEQUENCE
    distmat     Create a distance matrix from a multiple sequence alignment
    ednacomp    DNA compatibility algorithm
    ednadist    Nucleic acid sequence Distance Matrix program
    ednainvar   Nucleic acid sequence Invariants method
    ednaml      Phylogenies from nucleic acid Maximum Likelihood
    ednamlk     Phylogenies from nucleic acid Maximum Likelihood with clock
    ednapars    DNA parsimony algorithm
    ednapenny   Penny algorithm for DNA
    eprotdist   Protein distance algorithm
    eprotpars   Protein parsimony algorithm
    erestml     Restriction site Maximum Likelihood method
    eseqboot    Bootstrapped sequences algorithm
    fdiscboot   Bootstrapped discrete sites algorithm
    fdnacomp    DNA compatibility algorithm
    fdnadist    Nucleic acid sequence Distance Matrix program
    fdnainvar   Nucleic acid sequence Invariants method
    fdnaml      Estimates nucleotide phylogeny by maximum likelihood
    fdnamlk     Estimates nucleotide phylogeny by maximum likelihood
    fdnamove    Interactive DNA parsimony
    fdnapars    DNA parsimony algorithm
    fdnapenny   Penny algorithm for DNA
    fdolmove    Interactive Dollo or Polymorphism Parsimony
    ffreqboot   Bootstrapped genetic frequencies algorithm
    fproml      Protein phylogeny by maximum likelihood
    fpromlk     Protein phylogeny by maximum likelihood
    fprotdist   Protein distance algorithm
    fprotpars   Protein parsimony algorithm
    frestboot   Bootstrapped restriction sites algorithm
    frestdist   Distance matrix from restriction sites or fragments
    frestml     Restriction site maximum Likelihood method
    fseqboot    Bootstrapped sequences algorithm
    fseqbootall Bootstrapped sequences algorithm

    PHYLOGENY TREE DRAWING
    fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram
    fdrawtree Plots an unrooted tree diagram
    fretree   Interactive tree rearrangement

    PROTEIN 2D STRUCTURE
    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
    topo           Draws an image of a transmembrane protein

    PROTEIN 3D STRUCTURE
    contacts    Generate intra-chain CON files from CCF files
    domainalign Generate alignments (DAF file) for nodes in a DCF file
    domainrep   Reorder DCF file to identify representative structures
    domainreso  Remove low resolution domains from a DCF file
    interface   Generate inter-chain CON files from CCF files
    libgen      Generate discriminating elements from alignments
    matgen3d    Generate a 3D-1D scoring matrix from CCF files
    psiphi      Calculates phi and psi torsion angles from protein coordinates
    rocon       Generates a hits file from comparing two DHF files
    rocplot     Performs ROC analysis on hits files
    seqalign    Extend alignments (DAF file) with sequences (DHF file)
    seqfraggle  Removes fragment sequences from DHF files
    seqsearch   Generate PSI-BLAST hits (DHF file) from a DAF file
    seqsort     Remove ambiguous classified sequences from DHF files
    seqwords    Generates DHF files from keyword search of UniProt
    siggen      Generates a sparse protein signature from an alignment
    siggenlig   Generates ligand-binding signatures from a CON file
    sigscan     Generates hits (DHF file) from a signature search
    sigscanlig  Searches ligand-signature library & writes hits (LHF file)

    PROTEIN COMPOSITION
    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)

    PROTEIN MOTIFS
    antigenic      Finds antigenic sites in proteins
    digest         Reports on protein proteolytic enzyme or reagent cleavage sites
    echlorop       Reports presence of chloroplast transit peptides
    eiprscan       Motif detection
    elipop         Prediction of lipoproteins
    emast          Motif detection
    ememe          Multiple EM for Motif Elicitation
    ememetext      Multiple EM for Motif Elicitation. Text file only
    enetnglyc      Reports N-glycosylation sites in human proteins
    enetoglyc      Reports mucin type GalNAc O-glycosylation sites in mammalian prot
    eins
    enetphos       Reports ser, thr and tyr phosphorylation sites in eukaryotic prot
    eins
    epestfind      Finds PEST motifs as potential proteolytic cleavage sites
    eprop          Reports propeptide cleavage sites in proteins
    esignalp       Reports protein signal cleavage sites
    etmhmm         Reports transmembrane helices
    eyinoyang      Reports O-(beta)-GlcNAc attachment 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
    omeme          Motif detection
    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 datab
    ase
    sigcleave      Reports on signal cleavage sites in a protein sequence

    PROTEIN MUTATION
    msbar      Mutate a sequence
    shuffleseq Shuffles a set of sequences maintaining composition

    PROTEIN PROFILES
    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

    TEST
    crystalball Answers every drug discovery question about a sequence
    ensembltest Demonstration of the Ensembl API to be
    sqltest     Demonstration of SQL server access

    UTILS DATABASE CREATION
    aaindexextract Extract amino acid property data from AAINDEX
    allversusall   Sequence similarity data from all-versus-all comparison
    cathparse      Generates DCF file from raw CATH files
    cutgextract    Extract codon usage tables from CUTG database
    domainer       Generates domain CCF files from protein CCF files
    domainnr       Removes redundant domains from a DCF file
    domainseqs     Adds sequence records to a DCF file
    domainsse      Add secondary structure records to a DCF file
    hetparse       Converts heterogen group dictionary to EMBL-like format
    jaspextract    Extract data from JASPAR
    pdbparse       Parses PDB files and writes protein CCF files
    pdbplus        Add accessibility & secondary structure to a CCF file
    pdbtosp        Convert swissprot:PDB codes file to EMBL-like format
    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 applica
    tions
    scopparse      Generate DCF file from raw SCOP files
    seqnr          Removes redundancy from DHF files
    sites          Generate residue-ligand CON files from CCF files
    ssematch       Search a DCF file for secondary structure matches
    tfextract      Process TRANSFAC transcription factor database for use by tfscan

    UTILS DATABASE INDEXING
    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

    UTILS MISC
    embossdata    Find and retrieve EMBOSS data files
    embossversion Reports the current EMBOSS version number

       Example 3

       Display an alphabetic listing of all programs:

    % wossname -search '' -alphabetic
    Finds programs by keywords in their short description

    ALPHABETIC LIST OF PROGRAMS
    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
    allversusall   Sequence similarity data from all-versus-all comparison
    antigenic      Finds antigenic sites in proteins
    backtranambig  Back-translate a protein sequence to ambiguous nucleotide sequenc
    e
    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
    cathparse      Generates DCF file from raw CATH files
    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
    contacts       Generate intra-chain CON files from CCF files
    cpgplot        Identify and plot CpG islands in nucleotide sequence(s)
    cpgreport      Identify and report CpG-rich regions in nucleotide sequence(s)
    crystalball    Answers every drug discovery question about a sequence
    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
    domainalign    Generate alignments (DAF file) for nodes in a DCF file
    domainer       Generates domain CCF files from protein CCF files
    domainnr       Removes redundant domains from a DCF file
    domainrep      Reorder DCF file to identify representative structures
    domainreso     Remove low resolution domains from a DCF file
    domainseqs     Adds sequence records to a DCF file
    domainsse      Add secondary structure records to a DCF file
    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)
    echlorop       Reports presence of chloroplast transit peptides
    eclique        Largest clique program
    econsense      Majority-rule and strict consensus tree
    econtml        Continuous character Maximum Likelihood method
    econtrast      Continuous character Contrasts
    edialign       Local multiple alignment of sequences
    ednacomp       DNA compatibility algorithm
    ednadist       Nucleic acid sequence Distance Matrix program
    ednainvar      Nucleic acid sequence Invariants method
    ednaml         Phylogenies from nucleic acid Maximum Likelihood
    ednamlk        Phylogenies from nucleic acid Maximum Likelihood with clock
    ednapars       DNA parsimony algorithm
    ednapenny      Penny algorithm for DNA
    edollop        Dollo and polymorphism parsimony algorithm
    edolpenny      Penny algorithm Dollo or polymorphism
    efactor        Multistate to binary recoding program
    efitch         Fitch-Margoliash and Least-Squares Distance Methods
    egendist       Genetic Distance Matrix program
    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
    einverted      Finds inverted repeats in nucleotide sequences
    eiprscan       Motif detection
    ekitsch        Fitch-Margoliash method with contemporary tips
    elipop         Prediction of lipoproteins
    emast          Motif detection
    embossdata     Find and retrieve EMBOSS data files
    embossversion  Reports the current EMBOSS version number
    ememe          Multiple EM for Motif Elicitation
    ememetext      Multiple EM for Motif Elicitation. Text file only
    emira          MIRA fragment assembly program
    emiraest       MIRAest fragment assembly program
    emix           Mixed parsimony algorithm
    emma           Multiple sequence alignment (ClustalW wrapper)
    emnu           Simple menu of EMBOSS applications
    emowse         Search protein sequences by digest fragment molecular weight
    eneighbor      Phylogenies from distance matrix by N-J or UPGMA method
    enetnglyc      Reports N-glycosylation sites in human proteins
    enetoglyc      Reports mucin type GalNAc O-glycosylation sites in mammalian prot
    eins
    enetphos       Reports ser, thr and tyr phosphorylation sites in eukaryotic prot
    eins
    ensembltest    Demonstration of the Ensembl API to be
    entret         Retrieves sequence entries from flatfile databases and files
    epenny         Penny algorithm, branch-and-bound
    epestfind      Finds PEST motifs as potential proteolytic cleavage sites
    eprimer3       Picks PCR primers and hybridization oligos
    eprop          Reports propeptide cleavage sites in proteins
    eprotdist      Protein distance algorithm
    eprotpars      Protein parsimony algorithm
    equicktandem   Finds tandem repeats in nucleotide sequences
    erestml        Restriction site Maximum Likelihood method
    eseqboot       Bootstrapped sequences algorithm
    esignalp       Reports protein signal cleavage sites
    esim4          Align an mRNA to a genomic DNA sequence
    est2genome     Align EST sequences to genomic DNA sequence
    etandem        Finds tandem repeats in a nucleotide sequence
    etmhmm         Reports transmembrane helices
    extractalign   Extract regions from a sequence alignment
    extractfeat    Extract features from sequence(s)
    extractseq     Extract regions from a sequence
    eyinoyang      Reports O-(beta)-GlcNAc attachment sites
    fclique        Largest clique program
    fconsense      Majority-rule and strict consensus tree
    fcontml        Gene frequency and continuous character Maximum Likelihood
    fcontrast      Continuous character Contrasts
    fdiscboot      Bootstrapped discrete sites algorithm
    fdnacomp       DNA compatibility algorithm
    fdnadist       Nucleic acid sequence Distance Matrix program
    fdnainvar      Nucleic acid sequence Invariants method
    fdnaml         Estimates nucleotide phylogeny by maximum likelihood
    fdnamlk        Estimates nucleotide phylogeny by maximum likelihood
    fdnamove       Interactive DNA parsimony
    fdnapars       DNA parsimony algorithm
    fdnapenny      Penny algorithm for DNA
    fdollop        Dollo and polymorphism parsimony algorithm
    fdolmove       Interactive Dollo or Polymorphism Parsimony
    fdolpenny      Penny algorithm Dollo or polymorphism
    fdrawgram      Plots a cladogram- or phenogram-like rooted tree diagram
    fdrawtree      Plots an unrooted tree diagram
    featcopy       Reads and writes a feature table
    featreport     Reads and writes a feature table
    ffactor        Multistate to binary recoding program
    ffitch         Fitch-Margoliash and Least-Squares Distance Methods
    ffreqboot      Bootstrapped genetic frequencies algorithm
    fgendist       Compute genetic distances from gene frequencies
    findkm         Calculate and plot enzyme reaction data
    fkitsch        Fitch-Margoliash method with contemporary tips
    fmix           Mixed parsimony algorithm
    fmove          Interactive mixed method parsimony
    fneighbor      Phylogenies from distance matrix by N-J or UPGMA method
    fpars          Discrete character parsimony
    fpenny         Penny algorithm, branch-and-bound
    fproml         Protein phylogeny by maximum likelihood
    fpromlk        Protein phylogeny by maximum likelihood
    fprotdist      Protein distance algorithm
    fprotpars      Protein parsimony algorithm
    freak          Generate residue/base frequency table or plot
    frestboot      Bootstrapped restriction sites algorithm
    frestdist      Distance matrix from restriction sites or fragments
    frestml        Restriction site maximum Likelihood method
    fretree        Interactive tree rearrangement
    fseqboot       Bootstrapped sequences algorithm
    fseqbootall    Bootstrapped sequences algorithm
    ftreedist      Distances between trees
    ftreedistpair  Distances between two sets of trees
    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
    hetparse       Converts heterogen group dictionary to EMBL-like format
    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
    interface      Generate inter-chain CON files from CCF files
    isochore       Plots isochores in DNA sequences
    jaspextract    Extract data from JASPAR
    jaspscan       Scans DNA sequences for transcription factors
    libgen         Generate discriminating elements from alignments
    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 sequenc
    es
    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
    matgen3d       Generate a 3D-1D scoring matrix from CCF files
    megamerger     Merge two large overlapping DNA sequences
    merger         Merge two overlapping sequences
    msbar          Mutate a sequence
    mse            Multiple Sequence Editor
    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
    oalistat       Statistics for multiple alignment files
    octanol        Draw a White-Wimley protein hydropathy plot
    oddcomp        Identify proteins with specified sequence word composition
    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
    omeme          Motif detection
    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
    pdbparse       Parses PDB files and writes protein CCF files
    pdbplus        Add accessibility & secondary structure to a CCF file
    pdbtosp        Convert swissprot:PDB codes file to EMBL-like format
    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 datab
    ase
    psiphi         Calculates phi and psi torsion angles from protein coordinates
    rebaseextract  Process the REBASE database for use by restriction enzyme applica
    tions
    recoder        Find restriction sites to remove (mutate) with no translation cha
    nge
    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
    rocon          Generates a hits file from comparing two DHF files
    rocplot        Performs ROC analysis on hits files
    scopparse      Generate DCF file from raw SCOP files
    seealso        Finds programs with similar function to a specified program
    seqalign       Extend alignments (DAF file) with sequences (DHF file)
    seqfraggle     Removes fragment sequences from DHF files
    seqmatchall    All-against-all word comparison of a sequence set
    seqnr          Removes redundancy from DHF files
    seqret         Reads and writes (returns) sequences
    seqretsetall   Reads and writes (returns) many sets of sequences
    seqretsplit    Reads sequences and writes them to individual files
    seqsearch      Generate PSI-BLAST hits (DHF file) from a DAF file
    seqsort        Remove ambiguous classified sequences from DHF files
    seqwords       Generates DHF files from keyword search of UniProt
    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
    siggen         Generates a sparse protein signature from an alignment
    siggenlig      Generates ligand-binding signatures from a CON file
    sigscan        Generates hits (DHF file) from a signature search
    sigscanlig     Searches ligand-signature library & writes hits (LHF file)
    silent         Find restriction sites to insert (mutate) with no translation cha
    nge
    sirna          Finds siRNA duplexes in mRNA
    sites          Generate residue-ligand CON files from CCF files
    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
    sqltest        Demonstration of SQL server access
    ssematch       Search a DCF file for secondary structure matches
    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 sequen
    ces
    syco           Draw synonymous codon usage statistic plot for a nucleotide seque
    nce
    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
    topo           Draws an image of a transmembrane protein
    tranalign      Generate an alignment of nucleic coding regions from aligned prot
    eins
    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)
    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
    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

       Example 4

       Display only the groups that the programs can belong to:

    % wossname -search '' -groups
    Finds programs by keywords in their short description

    ACD
    ALIGNMENT CONSENSUS
    ALIGNMENT DIFFERENCES
    ALIGNMENT DOT PLOTS
    ALIGNMENT GLOBAL
    ALIGNMENT LOCAL
    ALIGNMENT MULTIPLE
    ASSEMBLY FRAGMENT ASSEMBLY
    DISPLAY
    EDIT
    ENZYME KINETICS
    FEATURE TABLES
    HMM
    INFORMATION
    MENUS
    NUCLEIC 2D STRUCTURE
    NUCLEIC CODON USAGE
    NUCLEIC COMPOSITION
    NUCLEIC CPG ISLANDS
    NUCLEIC GENE FINDING
    NUCLEIC MOTIFS
    NUCLEIC MUTATION
    NUCLEIC PRIMERS
    NUCLEIC PROFILES
    NUCLEIC REPEATS
    NUCLEIC RESTRICTION
    NUCLEIC RNA FOLDING
    NUCLEIC TRANSCRIPTION
    NUCLEIC TRANSLATION
    PHYLOGENY CONSENSUS
    PHYLOGENY CONTINUOUS CHARACTERS
    PHYLOGENY DISCRETE CHARACTERS
    PHYLOGENY DISTANCE MATRIX
    PHYLOGENY GENE FREQUENCIES
    PHYLOGENY MOLECULAR SEQUENCE
    PHYLOGENY TREE DRAWING
    PROTEIN 2D STRUCTURE
    PROTEIN 3D STRUCTURE
    PROTEIN COMPOSITION
    PROTEIN MOTIFS
    PROTEIN MUTATION
    PROTEIN PROFILES
    TEST
    UTILS DATABASE CREATION
    UTILS DATABASE INDEXING
    UTILS MISC

       Example 5

       Output html tags around the list of programs:

    % wossname '' -html -out wossname.html
    Finds programs by keywords in their short description

       Go to the output files for this example

    Command line arguments

    Finds programs by keywords in their short description
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers:
      [-search]            string     Enter a word or words here and a
                                      case-independent search for it will be made
                                      in the one-line documentation, group names
                                      and keywords of all of the EMBOSS programs.
                                      If no keyword is specified, all programs
                                      will be listed. (Any string)

       Additional (Optional) qualifiers:
       -explode            boolean    [N] The groups that EMBOSS applications
                                      belong to have two forms, exploded and not
                                      exploded. The exploded group names are more
                                      numerous and often vaguely phrased than the
                                      non-exploded ones. The exploded names are
                                      formed from definitions of the group names
                                      that start like NAME1:NAME2 and which are
                                      then expanded into many combinations of the
                                      names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
                                      NAME2 NAME1'. The non-expanded names are
                                      simply like: 'NAME1 NAME2'.
       -[no]allmatch       boolean    [Y] By default, all words in the search
                                      string must match. This option searches for
                                      a match to any word in a list of
                                      possibilities
       -showkeywords       boolean    [N] Show keywords with program documentation
       -outfile            outfile    [stdout] Output file name
       -html               toggle     [N] If you are sending the output to a file,
                                      this will format it for displaying as a
                                      table in a WWW document.
       -groups             boolean    [N] If you use this option, then only the
                                      group names will output to the file
       -alphabetic         boolean    [N] If you use this option, then you will
                                      get a single list of the program names and
                                      descriptions instead of the programs being
                                      listed in their functional groups.

       Advanced (Unprompted) qualifiers:
       -[no]emboss         boolean    [Y] If you use this option then EMBOSS
                                      program documentation will be searched. If
                                      this option is set to be false, then only
                                      the EMBASSY programs will be searched (if
                                      the -embassy option is true). EMBASSY
                                      programs are not strictly part of EMBOSS,
                                      but use the same code libraries and share
                                      the same look and feel, but are generally
                                      developed by people who wish the programs to
                                      be outside of the GNU Public Licence scheme
       -[no]embassy        boolean    [Y] If you use this option then EMBASSY
                                      program documentation will be searched. If
                                      this option is set to be false, then only
                                      the EMBOSS programs will be searched (if the
                                      -emboss option is true). EMBASSY programs
                                      are not strictly part of EMBOSS, but use the
                                      same code libraries and share the same look
                                      and feel, but are generally developed by
                                      people who wish the programs to be outside
                                      of the GNU Public Licence scheme
       -showembassy        string     If you use this option then this EMBASSY
                                      package program documentation will be
                                      searched. EMBASSY programs are not strictly
                                      part of EMBOSS, but use the same code
                                      libraries and share the same look and feel,
                                      but are generally developed by people who
                                      wish the programs to be outside of the GNU
                                      Public Licence scheme (Any string)
       -colon              boolean    [N] The groups that EMBOSS applications
                                      belong to up to two levels, for example the
                                      primary group 'ALIGNMENT' has several
                                      sub-groups, or second-level groups, e.g.:
                                      CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
                                      LOCAL, MULTIPLE. To aid programs that parse
                                      the output of wossname that require the
                                      names of these subgroups, a colon ':' will
                                      be placed between the first and second level
                                      of the group name if this option is true.
                                      Note: This does not apply if the group names
                                      have been exploded with the 'explode'
                                      option.
       -gui                boolean    [N] This option is intended to help those
                                      who are designing Graphical User Interfaces
                                      to the EMBOSS applications. Some EMBOSS
                                      programs are inappropriate for running in a
                                      GUI, these include other menu programs and
                                      interactive editors. This option allows you
                                      to only report those programs that can be
                                      run from a GUI

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

    Input file format

       wossname reads the brief descriptions and the program groups from the
       ACD files. (ACD files control the parameters that the programs expect -
       don't worry about them unless you are writing EMBOSS programs).

       The format of ACD files is documented elsewhere.

    Output file format

       The results are written out as a simple list preceded by the group that
       the programs belong to or the word that is being searched for.

      Output files for usage example 5

      File: wossname.html

       ACD  Program name 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   ALIGNMENT
       CONSENSUS
       Program name 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   [Part of this file has been
       deleted for brevity]  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   UTILS
       MISC
       Program name Description  embossdata Find and retrieve EMBOSS
       data files   embossversion Reports the
       current EMBOSS version number

       If the -html, -prelink and -postlink qualifiers are specified, then the
       output will be wrapped in HTML tags, ready for inclusion in a Web page.
       Note that tags such as , ,  and  are not
       output by this program as the list of programs is expected to form only
       part of the contents of a web page - the rest of the web page must be
       supplied by the user.

    Data files

       As noted above, the program ACD files are searched. The average user
       will not need to worry about this.

    Notes

       wossname reads the short descriptions and the program groups from the
       program ACD files. These file describe the command-line interface of
       the applications. You don't need to know about them unless you are
       writing EMBOSS programs. They are described in the EMBOSS Developers
       Manual.

       If a program's ACD file does not specify a program group, then it will
       be automatically assigned to the group ASSORTED in the output file. A
       program can belong to more than one group.

    References

       None.

    Warnings

       None.

    Diagnostic Error Messages

       None.

    Exit status

       It always exits with status 0

    Known bugs

       None.

    See also

                        Program name                          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

    Author(s)

       Gary             Williams (gwilliam (c) rfcgr.mrc.ac.uk)
       MRC              Rosalind Franklin Centre for Genomics Research Wellcome Trust
       Genome           Campus, Hinxton, Cambridge, CB10 1SB, UK

    History

    Target users

                        This program is intended to be used by everyone and everything, from
                        naive users to embedded scripts.

    Comments

                        None

## Command line arguments

    Displays full documentation for an application
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers:
      [-program]           string     Enter the name of an EMBOSS program (Any
                                      string of at least 1 characters)

       Additional (Optional) qualifiers:
       -outfile            outfile    [stdout] Program documentation text output
                                      file
       -html               boolean    [N] This will format the output for
                                      displaying as a WWW document.
       -more               boolean    [@(!$(html))] This uses the standard UNIX
                                      utility 'more' to display the text
                                      page-by-page, waiting for you to read one
                                      screen-full before going on to the next
                                      page. When you have finished reading a page,
                                      press the SPACE bar to proceed to the next
                                      page.

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-program] (Parameter 1) | string | Enter the name of an EMBOSS program | Any string of at least 1 characters | Required
Additional (Optional) qualifiers
-outfile | outfile | Program documentation text output file | Output file | stdout
-html | boolean | This will format the output for displaying as a WWW document. | Boolean value Yes/No | No
-more | boolean | This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page. | Boolean value Yes/No | @(!$(html))
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

None.

## Output file format

Text documentation is output.

The table of command line arguments can be a bit difficult to read. This is the result of changing HTML Web pages to text.

You will see a page of documentation on the wossname program. To see further pages, you should press the SPACE bar on your keyboard. To stop seeing the documentation before you get to the end of the text, you can press the key q to quit.

## Data files

The original data for the documentation can be found in: http://emboss.sourceforge.net/apps/ but please note that this is the documentation for the current development version. The documentation for your release should be nistalled somewhere on your system.

## Notes

The documentation for your own release is included as HTML pages in the EMBOSS distribution and may be available at your site. The same documentation is also available however through the program tfm as plain text. The documentation for all current and some past releases is provided by the developers at http://emboss.sourceforge.net/apps/. All EMBOSS programs should be adequately described. If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@emboss.open-bio.org).

The unusual name of this program comes from the common computing science expression: RTFM. This acronym, as you probably already know, stands for Read The Fine* Manual; so this is The Fine* Manual. (* Insert the expletive of your choice here!)

Paged text output to the screen

tfm is unusual for an EMBOSS program in that it expects to be used interactively and so it displays the documentation text a page at a time, pausing after every page for the user to press the SPACE bar on their keyboard, i.e. it uses the UNIX program `more` to display the information. This behaviour can be turned off by using the qualifier -nomore.

The program `more` is a very standard way for text files to be displayed in UNIX. You might, however, prefer the text to be displayed using other programs, for example `less` (which has more functionality than `more` and is used by many people). The UNIX environment variable `PAGER` can be set to hold the name of your preferred program. If you have PAGER set, then tfm will use this specified program instead of using the default `more` program. (If you want tfm to use a specified program that is different to the normal `PAGER` program, then `PAGER` can be overriden by setting the environment variable `EMBOSS_PAGER` to hold the name of the program that should only be used to display text in tfm). `PAGER` can be set in UNIX with `setenv PAGER less`.

To get help on `more` when using it to display text, press the `?` key. To get help on `less` when using it to display text, press the `h` key.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

tfm will warn you if you have supplied the name of a program which is not documented yet or which doesn't exist in EMBOSS.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | 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)
whichdb | Search all sequence databases for an entry and retrieve it
wossname | Finds programs by keywords in their short description

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written: 4 Aug 2000.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None