EMBOSS

| tfm

## 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

    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 appl
    ications
    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 seque
    nce
    restover         Find restriction enzymes producing a specific overhang
    restrict         Report restriction enzyme cleavage sites in a nucleotide seque
    nce
    showseq          Displays sequences with features in pretty format
    silent           Find restriction sites to insert (mutate) with no translation
    change

       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 f
    ile
    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 ambiguouos consensus sequence from a multiple alignm
    ent
    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
    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 seq
    uences
    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 aligment of nucleic coding regions from aligned pr
    oteins

    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 seque
    nce
    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
    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 sequen
    ces
    pasteseq         Insert one sequence into another
    revseq           Reverse and complement a nucleotide sequence
    seqret           Reads and writes (returns) 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
    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 statictic plot for a nucleotide se
    quence

    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 sequenc
    e
    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 DNA 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 sequ
    ences
    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 statictic plot for a nucleotide se
    quence
    tcode            Identify protein-coding regions using Fickett TESTCODE statist
    ic
    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 sequ
    ences

    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 seque
    nce
    restover         Find restriction enzymes producing a specific overhang
    restrict         Report restriction enzyme cleavage sites in a nucleotide seque
    nce
    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 sequ
    ence
    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 seque
    nce
    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        Generate ligand-binding signatures from a CON file
    sigscan          Generate hits (DHF file) from a signature search
    sigscanlig       Search ligand-signature library & write hits (LHF file)

    PROTEIN COMPOSITION
    backtranambig    Back-translate a protein sequence to ambiguous nucleotide sequ
    ence
    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 Kyte-Doolittle hydropathy plot for a protein sequence
    pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein alignment
    wordcount        Count and extract unique words in DNA sequence(s)

    PROTEIN MOTIFS
    antigenic        Finds antigenic sites in proteins
    digest           Reports on protein proteolytic enzyme or reagent cleavage site
    s
    echlorop         Reports presence of chloroplast transit peptides
    eiprscan         Motif detection
    elipop           Prediction of lipoproteins
    emast            Motif detection
    ememe            Motif detection
    enetnglyc        Reports N-glycosylation sites in human proteins
    enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian p
    roteins
    enetphos         Reports ser, thr and tyr phosphorylation sites in eukaryotic p
    roteins
    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 da
    tabase
    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
    myseq            Demonstration of sequence reading
    mytest           Demonstration of sequence reading

    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 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 appl
    ications
    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 tfsc
    an

    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    Writes the current EMBOSS version number to a file

       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 f
    ile
    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 sequ
    ence
    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 sequenc
    e
    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 ambiguouos consensus sequence from a multiple alignm
    ent
    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 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 site
    s
    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    Writes the current EMBOSS version number to a file
    ememe            Motif detection
    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 p
    roteins
    enetphos         Reports ser, thr and tyr phosphorylation sites in eukaryotic p
    roteins
    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 sequ
    ences
    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
    myseq            Demonstration of sequence reading
    mytest           Demonstration of sequence reading
    needle           Needleman-Wunsch global alignment of two sequences
    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 sequen
    ces
    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 Kyte-Doolittle 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 da
    tabase
    psiphi           Calculates phi and psi torsion angles from protein coordinates
    rebaseextract    Process the REBASE database for use by restriction enzyme appl
    ications
    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 seque
    nce
    restover         Find restriction enzymes producing a specific overhang
    restrict         Report restriction enzyme cleavage sites in a nucleotide seque
    nce
    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
    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
    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        Generate ligand-binding signatures from a CON file
    sigscan          Generate hits (DHF file) from a signature search
    sigscanlig       Search ligand-signature library & write hits (LHF file)
    silent           Find restriction sites to insert (mutate) with no translation
    change
    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
    splitter         Split sequence(s) into smaller sequences
    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 seq
    uences
    syco             Draw synonymous codon usage statictic plot for a nucleotide se
    quence
    tcode            Identify protein-coding regions using Fickett TESTCODE statist
    ic
    textsearch       Search the textual description of sequence(s)
    tfextract        Process TRANSFAC transcription factor database for use by tfsc
    an
    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 aligment of nucleic coding regions from aligned pr
    oteins
    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 DNA 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

       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 is accepted)

       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 is
                                      accepted)
       -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. 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

    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 ambiguouos
       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 Writes the
       current EMBOSS version number to a file

       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 © 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

       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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-program] (Parameter 1) | Enter the name of an EMBOSS program | Any string of at least 1 characters | Required
Additional (Optional) qualifiers | Allowed values | Default
-outfile | Program documentation text output file | Output file | stdout
-html | This will format the output for displaying as a WWW document. | Boolean value Yes/No | No
-more | 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 | Allowed values | Default
(none)

## 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