EMBOSS

| tfm

## Function

Displays a program's help documentation manual

## Description

This program displays the help documentation for an EMBOSS program.

The contributors of the EMBOSS programs do attempt to provide an adequate description of the programs. This documentation for your current release is included as HTML pages in the EMBOSS distribution and may be available at your site. The latest documentation for the next release is provided by the developers at http://emboss.sourceforge.net/apps/

The release documentation is also available however through the program tfm as normal text.

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 text is paged to the screen using the UNIX program 'more'. 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 by a command like:
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.

## Usage

Here is a sample session with tfm

##

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    % tfm wossname
    Displays a program's help documentation manual

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

                                     wossname

    Function

       Finds programs by keywords in their one-line documentation

    Description

       This allows a user to search for keywords or parts of words in the
       brief documentation (as displayed by a program when it first starts).
       The program name and the brief description is output. If no words to
       search for are specified, then details of all the EMBOSS programs are
       output.

       The program has been written on the assumption that most people will
       use it to quickly find the name of a program based on that program's
       description, so the output goes to the screen by default.

       This program may find some use in automatically generating lists of
       EMBOSS programs and their groups for Web pages.

    Usage

       Here is a sample session with wossname

       Search for programs with 'restrict' in their description:

    % wossname restrict
    Finds programs by keywords in their one-line documentation

    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
    recoder          Remove restriction sites but maintain same translation
    redata           Search REBASE for enzyme name, references, suppliers etc
    remap            Display sequence with restriction sites, translation etc
    restover         Find restriction enzymes producing specific overhang
    restrict         Finds restriction enzyme cleavage sites
    showseq          Display a sequence with features, translation etc
    silent           Silent mutation restriction enzyme scan

       Example 2

       Display a listing of programs in their groups:

    % wossname -search ''
    Finds programs by keywords in their one-line documentation

    ACD
    acdc             ACD compiler
    acdpretty        ACD pretty printing utility
    acdtable         Creates an HTML table from an ACD file
    acdtrace         ACD compiler on-screen trace
    acdvalid         ACD file validation

    ALIGNMENT CONSENSUS
    cons             Creates a consensus from multiple alignments
    megamerger       Merge two large overlapping nucleic acid sequences
    merger           Merge two overlapping sequences

    ALIGNMENT DIFFERENCES
    diffseq          Find differences between nearly identical sequences

    ALIGNMENT DOT PLOTS
    dotmatcher       Displays a thresholded dotplot of two sequences
    dotpath          Non-overlapping wordmatch dotplot of two sequences
    dottup           Displays a wordmatch dotplot of two sequences
    polydot          Displays all-against-all dotplots of a set of sequences

    ALIGNMENT GLOBAL
    esim4            Align an mRNA to a genomic DNA sequence
    est2genome       Align EST and genomic DNA sequences
    needle           Needleman-Wunsch global alignment
    stretcher        Finds the best global alignment between two sequences

    ALIGNMENT LOCAL
    matcher          Finds the best local alignments between two sequences
    seqmatchall      All-against-all comparison of a set of sequences
    supermatcher     Match large sequences against one or more other sequences
    water            Smith-Waterman local alignment
    wordfinder       Match large sequences against one or more other sequences
    wordmatch        Finds all exact matches of a given size between 2 sequences

    ALIGNMENT MULTIPLE
    edialign         Local multiple alignment of sequences
    emma             Multiple alignment program - interface to ClustalW program
    infoalign        Information on a multiple sequence alignment
    mse              Multiple Sequence Editor
    plotcon          Plot quality of conservation of a sequence alignment
    prettyplot       Displays aligned sequences, with colouring and boxing
    showalign        Displays a multiple sequence alignment
    tranalign        Align nucleic coding regions given the aligned proteins

    DISPLAY
    abiview          Reads ABI file and display the trace
    cirdna           Draws circular maps of DNA constructs
    lindna           Draws linear maps of DNA constructs
    pepnet           Displays proteins as a helical net
    pepwheel         Shows protein sequences as helices
    prettyplot       Displays aligned sequences, with colouring and boxing
    prettyseq        Output sequence with translated ranges
    remap            Display sequence with restriction sites, translation etc
    seealso          Finds programs sharing group names
    showalign        Displays a multiple sequence alignment
    showdb           Displays information on the currently available databases
    showfeat         Show features of a sequence
    showseq          Display a sequence with features, translation etc
    sixpack          Display a DNA sequence with 6-frame translation and ORFs
    textsearch       Search sequence documentation. Slow, use SRS and Entrez!

    EDIT
    biosed           Replace or delete sequence sections
    codcopy          Reads and writes a codon usage table
    cutseq           Removes a specified section from a sequence
    degapseq         Removes gap characters from sequences
    descseq          Alter the name or description of a sequence
    entret           Reads and writes (returns) flatfile entries
    extractalign     Extract regions from a sequence alignment
    extractfeat      Extract features from a sequence
    extractseq       Extract regions from a sequence
    listor           Write a list file of the logical OR of two sets of sequences
    makenucseq       Creates random nucleotide sequences
    makeprotseq      Creates random protein sequences
    maskfeat         Mask off features of a sequence
    maskseq          Mask off regions of a sequence
    newseq           Type in a short new sequence
    noreturn         Removes carriage return from ASCII files
    notseq           Exclude a set of sequences and write out the remaining ones
    nthseq           Writes one sequence from a multiple set of sequences
    pasteseq         Insert one sequence into another
    revseq           Reverse and complement a sequence
    seqret           Reads and writes (returns) sequences
    seqretsplit      Reads and writes (returns) sequences in individual files
    skipseq          Reads and writes (returns) sequences, skipping first few
    splitter         Split a sequence into (overlapping) smaller sequences
    trimest          Trim poly-A tails off EST sequences
    trimseq          Trim ambiguous bits off the ends of sequences
    union            Reads sequence fragments and builds one sequence
    vectorstrip      Strips out DNA between a pair of vector sequences
    yank             Reads a sequence range, appends the full USA to a list file

    ENZYME KINETICS
    findkm           Find Km and Vmax for an enzyme reaction

    FEATURE TABLES
    coderet          Extract CDS, mRNA and translations from feature tables
    extractfeat      Extract features from a sequence
    maskfeat         Mask off features of a sequence
    showfeat         Show features of a sequence
    twofeat          Finds neighbouring pairs of features in sequences

    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        Information on a multiple sequence alignment
    infoseq          Displays some simple information about sequences
    seealso          Finds programs sharing group names
    showdb           Displays information on the currently available databases
    textsearch       Search sequence documentation. Slow, use SRS and Entrez!
    tfm              Displays a program's help documentation manual
    whichdb          Search all databases for an entry
    wossname         Finds programs by keywords in their one-line documentation

    MENUS
    emnu             Simple menu of EMBOSS applications

    NUCLEIC 2D STRUCTURE
    einverted        Finds DNA inverted repeats
    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              CAI codon adaptation index
    chips            Codon usage statistics
    codcmp           Codon usage table comparison
    cusp             Create a codon usage table
    syco             Synonymous codon usage Gribskov statistic plot

    NUCLEIC COMPOSITION
    banana           Bending and curvature plot in B-DNA
    btwisted         Calculates the twisting in a B-DNA sequence
    chaos            Create a chaos game representation plot for a sequence
    compseq          Count composition of dimer/trimer/etc words in a sequence
    dan              Calculates DNA RNA/DNA melting temperature
    freak            Residue/base frequency table or plot
    isochore         Plots isochores in large DNA sequences
    sirna            Finds siRNA duplexes in mRNA
    wordcount        Counts words of a specified size in a DNA sequence

    NUCLEIC CPG ISLANDS
    cpgplot          Plot CpG rich areas
    cpgreport        Reports all CpG rich regions
    geecee           Calculates fractional GC content of nucleic acid sequences
    newcpgreport     Report CpG rich areas
    newcpgseek       Reports CpG rich regions

    NUCLEIC GENE FINDING
    getorf           Finds and extracts open reading frames (ORFs)
    marscan          Finds MAR/SAR sites in nucleic sequences
    plotorf          Plot potential open reading frames
    showorf          Pretty output of DNA translations
    sixpack          Display a DNA sequence with 6-frame translation and ORFs
    syco             Synonymous codon usage Gribskov statistic plot
    tcode            Fickett TESTCODE statistic to identify protein-coding DNA
    wobble           Wobble base plot

    NUCLEIC MOTIFS
    dreg             Regular expression search of a nucleotide sequence
    fuzznuc          Nucleic acid pattern search
    fuzztran         Protein pattern search after translation
    marscan          Finds MAR/SAR sites in nucleic sequences

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

    NUCLEIC PRIMERS
    eprimer3         Picks PCR primers and hybridization oligos
    primersearch     Searches DNA sequences for matches with primer pairs
    stssearch        Search a DNA database for matches with a set of STS primers

    NUCLEIC PROFILES
    profit           Scan a sequence or database with a matrix or profile
    prophecy         Creates matrices/profiles from multiple alignments
    prophet          Gapped alignment for profiles

    NUCLEIC REPEATS
    einverted        Finds DNA inverted repeats
    equicktandem     Finds tandem repeats
    etandem          Looks for tandem repeats in a nucleotide sequence
    palindrome       Looks for inverted repeats in a nucleotide sequence

    NUCLEIC RESTRICTION
    recoder          Remove restriction sites but maintain same translation
    redata           Search REBASE for enzyme name, references, suppliers etc
    remap            Display sequence with restriction sites, translation etc
    restover         Find restriction enzymes producing specific overhang
    restrict         Finds restriction enzyme cleavage sites
    showseq          Display a sequence with features, translation etc
    silent           Silent mutation restriction enzyme scan

    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
    tfscan           Scans DNA sequences for transcription factors

    NUCLEIC TRANSLATION
    backtranambig    Back translate a protein sequence to ambiguous codons
    backtranseq      Back translate a protein sequence
    coderet          Extract CDS, mRNA and translations from feature tables
    plotorf          Plot potential open reading frames
    prettyseq        Output sequence with translated ranges
    remap            Display sequence with restriction sites, translation etc
    showorf          Pretty output of DNA translations
    showseq          Display a sequence with features, translation etc
    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          Creates a distance matrix from multiple alignments
    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
    helixturnhelix   Report nucleic acid binding motifs
    hmoment          Hydrophobic moment calculation
    pepcoil          Predicts coiled coil regions
    pepnet           Displays proteins as a helical net
    pepwheel         Shows protein sequences as helices
    tmap             Displays membrane spanning regions
    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           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 codons
    backtranseq      Back translate a protein sequence
    charge           Protein charge plot
    checktrans       Reports STOP codons and ORF statistics of a protein
    compseq          Count composition of dimer/trimer/etc words in a sequence
    emowse           Protein identification by mass spectrometry
    freak            Residue/base frequency table or plot
    iep              Calculates the isoelectric point of a protein
    mwcontam         Shows molwts that match across a set of files
    mwfilter         Filter noisy molwts from mass spec output
    octanol          Displays protein hydropathy
    pepinfo          Plots simple amino acid properties in parallel
    pepstats         Protein statistics
    pepwindow        Displays protein hydropathy
    pepwindowall     Displays protein hydropathy of a set of sequences

    PROTEIN MOTIFS
    antigenic        Finds antigenic sites in proteins
    digest           Protein proteolytic enzyme or reagent cleavage digest
    emast            Motif detection
    ememe            Motif detection
    epestfind        Finds PEST motifs as potential proteolytic cleavage sites
    fuzzpro          Protein pattern search
    fuzztran         Protein pattern search after translation
    helixturnhelix   Report nucleic acid binding motifs
    oddcomp          Find protein sequence regions with a biased composition
    omeme            Motif detection
    patmatdb         Search a protein sequence with a motif
    patmatmotifs     Search a PROSITE motif database with a protein sequence
    pepcoil          Predicts coiled coil regions
    preg             Regular expression search of a protein sequence
    pscan            Scans proteins using PRINTS
    sigcleave        Reports protein signal cleavage sites

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

    PROTEIN PROFILES
    profit           Scan a sequence or database with a matrix or profile
    prophecy         Creates matrices/profiles from multiple alignments
    prophet          Gapped alignment for profiles

    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 data from AAINDEX
    allversusall     Sequence similarity data from all-versus-all comparison
    cathparse        Generates DCF file from raw CATH files
    cutgextract      Extract data from CUTG
    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
    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
    prosextract      Build the PROSITE motif database for use by patmatmotifs
    rebaseextract    Extract data from REBASE
    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        Extract data from TRANSFAC

    UTILS DATABASE INDEXING
    dbiblast         Index a BLAST database
    dbifasta         Database indexing for fasta file databases
    dbiflat          Index a flat file database
    dbigcg           Index a GCG formatted database
    dbxfasta         Database b+tree indexing for fasta file databases
    dbxflat          Database b+tree indexing for flat file databases
    dbxgcg           Database b+tree indexing for GCG formatted databases

    UTILS MISC
    embossdata       Finds or fetches data files read by EMBOSS programs
    embossversion    Writes the current EMBOSS version number

       Example 3

       Display an alphabetic listing of all programs:

    % wossname -search '' -alphabetic
    Finds programs by keywords in their one-line documentation

    ALPHABETIC LIST OF PROGRAMS
    aaindexextract   Extract data from AAINDEX
    abiview          Reads ABI file and display the trace
    acdc             ACD compiler
    acdpretty        ACD pretty printing utility
    acdtable         Creates an HTML table from an ACD file
    acdtrace         ACD compiler on-screen trace
    acdvalid         ACD file validation
    allversusall     Sequence similarity data from all-versus-all comparison
    antigenic        Finds antigenic sites in proteins
    backtranambig    Back translate a protein sequence to ambiguous codons
    backtranseq      Back translate a protein sequence
    banana           Bending and curvature plot in B-DNA
    biosed           Replace or delete sequence sections
    btwisted         Calculates the twisting in a B-DNA sequence
    cai              CAI codon adaptation index
    cathparse        Generates DCF file from raw CATH files
    chaos            Create a chaos game representation plot for a sequence
    charge           Protein charge plot
    checktrans       Reports STOP codons and ORF statistics of a protein
    chips            Codon usage statistics
    cirdna           Draws circular maps of DNA constructs
    codcmp           Codon usage table comparison
    codcopy          Reads and writes a codon usage table
    coderet          Extract CDS, mRNA and translations from feature tables
    compseq          Count composition of dimer/trimer/etc words in a sequence
    cons             Creates a consensus from multiple alignments
    contacts         Generate intra-chain CON files from CCF files
    cpgplot          Plot CpG rich areas
    cpgreport        Reports all CpG rich regions
    crystalball      Answers every drug discovery question about a sequence
    cusp             Create a codon usage table
    cutgextract      Extract data from CUTG
    cutseq           Removes a specified section from a sequence
    dan              Calculates DNA RNA/DNA melting temperature
    dbiblast         Index a BLAST database
    dbifasta         Database indexing for fasta file databases
    dbiflat          Index a flat file database
    dbigcg           Index a GCG formatted database
    dbxfasta         Database b+tree indexing for fasta file databases
    dbxflat          Database b+tree indexing for flat file databases
    dbxgcg           Database b+tree indexing for GCG formatted databases
    degapseq         Removes gap characters from sequences
    descseq          Alter the name or description of a sequence
    diffseq          Find differences between nearly identical sequences
    digest           Protein proteolytic enzyme or reagent cleavage digest
    distmat          Creates a distance matrix from multiple alignments
    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       Displays a thresholded dotplot of two sequences
    dotpath          Non-overlapping wordmatch dotplot of two sequences
    dottup           Displays a wordmatch dotplot of two sequences
    dreg             Regular expression search of a nucleotide sequence
    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 DNA inverted repeats
    ekitsch          Fitch-Margoliash method with contemporary tips
    emast            Motif detection
    embossdata       Finds or fetches data files read by EMBOSS programs
    embossversion    Writes the current EMBOSS version number
    ememe            Motif detection
    emix             Mixed parsimony algorithm
    emma             Multiple alignment program - interface to ClustalW program
    emnu             Simple menu of EMBOSS applications
    emowse           Protein identification by mass spectrometry
    eneighbor        Phylogenies from distance matrix by N-J or UPGMA method
    entret           Reads and writes (returns) flatfile entries
    epenny           Penny algorithm, branch-and-bound
    epestfind        Finds PEST motifs as potential proteolytic cleavage sites
    eprimer3         Picks PCR primers and hybridization oligos
    eprotdist        Protein distance algorithm
    eprotpars        Protein parsimony algorithm
    equicktandem     Finds tandem repeats
    erestml          Restriction site Maximum Likelihood method
    eseqboot         Bootstrapped sequences algorithm
    esim4            Align an mRNA to a genomic DNA sequence
    est2genome       Align EST and genomic DNA sequences
    etandem          Looks for tandem repeats in a nucleotide sequence
    extractalign     Extract regions from a sequence alignment
    extractfeat      Extract features from a sequence
    extractseq       Extract regions from a sequence
    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
    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           Find Km and Vmax for an enzyme reaction
    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            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          Nucleic acid pattern search
    fuzzpro          Protein pattern search
    fuzztran         Protein pattern search after translation
    garnier          Predicts protein secondary structure
    geecee           Calculates fractional GC content of nucleic acid sequences
    getorf           Finds and extracts open reading frames (ORFs)
    helixturnhelix   Report nucleic acid binding motifs
    hetparse         Converts heterogen group dictionary to EMBL-like format
    hmoment          Hydrophobic moment calculation
    iep              Calculates the isoelectric point of a protein
    infoalign        Information on a multiple sequence alignment
    infoseq          Displays some simple information about sequences
    interface        Generate inter-chain CON files from CCF files
    isochore         Plots isochores in large DNA sequences
    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       Creates random nucleotide sequences
    makeprotseq      Creates random protein sequences
    marscan          Finds MAR/SAR sites in nucleic sequences
    maskfeat         Mask off features of a sequence
    maskseq          Mask off regions of a sequence
    matcher          Finds the best local alignments between two sequences
    matgen3d         Generate a 3D-1D scoring matrix from CCF files
    megamerger       Merge two large overlapping nucleic acid sequences
    merger           Merge two overlapping sequences
    msbar            Mutate sequence beyond all recognition
    mse              Multiple Sequence Editor
    mwcontam         Shows molwts that match across a set of files
    mwfilter         Filter noisy molwts from mass spec output
    myseq            Demonstration of sequence reading
    mytest           Demonstration of sequence reading
    needle           Needleman-Wunsch global alignment
    newcpgreport     Report CpG rich areas
    newcpgseek       Reports CpG rich regions
    newseq           Type in a short new sequence
    noreturn         Removes carriage return from ASCII files
    notseq           Exclude a set of sequences and write out the remaining ones
    nthseq           Writes one sequence from a multiple set of sequences
    oalistat         Statistics for multiple alignment files
    octanol          Displays protein hydropathy
    oddcomp          Find protein sequence regions with a biased 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       Looks for inverted repeats in a nucleotide sequence
    pasteseq         Insert one sequence into another
    patmatdb         Search a protein sequence with a motif
    patmatmotifs     Search a PROSITE motif database with a protein sequence
    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
    pepinfo          Plots simple amino acid properties in parallel
    pepnet           Displays proteins as a helical net
    pepstats         Protein statistics
    pepwheel         Shows protein sequences as helices
    pepwindow        Displays protein hydropathy
    pepwindowall     Displays protein hydropathy of a set of sequences
    plotcon          Plot quality of conservation of a sequence alignment
    plotorf          Plot potential open reading frames
    polydot          Displays all-against-all dotplots of a set of sequences
    preg             Regular expression search of a protein sequence
    prettyplot       Displays aligned sequences, with colouring and boxing
    prettyseq        Output sequence with translated ranges
    primersearch     Searches DNA sequences for matches with primer pairs
    printsextract    Extract data from PRINTS
    profit           Scan a sequence or database with a matrix or profile
    prophecy         Creates matrices/profiles from multiple alignments
    prophet          Gapped alignment for profiles
    prosextract      Build the PROSITE motif database for use by patmatmotifs
    pscan            Scans proteins using PRINTS
    psiphi           Phi and psi torsion angles from protein coordinates
    rebaseextract    Extract data from REBASE
    recoder          Remove restriction sites but maintain same translation
    redata           Search REBASE for enzyme name, references, suppliers etc
    remap            Display sequence with restriction sites, translation etc
    restover         Find restriction enzymes producing specific overhang
    restrict         Finds restriction enzyme cleavage sites
    revseq           Reverse and complement a 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 sharing group names
    seqalign         Extend alignments (DAF file) with sequences (DHF file)
    seqfraggle       Removes fragment sequences from DHF files
    seqmatchall      All-against-all comparison of a set of sequences
    seqnr            Removes redundancy from DHF files
    seqret           Reads and writes (returns) sequences
    seqretsplit      Reads and writes (returns) sequences in 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        Displays a multiple sequence alignment
    showdb           Displays information on the currently available databases
    showfeat         Show features of a sequence
    showorf          Pretty output of DNA translations
    showseq          Display a sequence with features, translation etc
    shuffleseq       Shuffles a set of sequences maintaining composition
    sigcleave        Reports protein signal cleavage sites
    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           Silent mutation restriction enzyme scan
    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
    skipseq          Reads and writes (returns) sequences, skipping first few
    splitter         Split a sequence into (overlapping) smaller sequences
    ssematch         Search a DCF file for secondary structure matches
    stretcher        Finds the best global alignment between two sequences
    stssearch        Search a DNA database for matches with a set of STS primers
    supermatcher     Match large sequences against one or more other sequences
    syco             Synonymous codon usage Gribskov statistic plot
    tcode            Fickett TESTCODE statistic to identify protein-coding DNA
    textsearch       Search sequence documentation. Slow, use SRS and Entrez!
    tfextract        Extract data from TRANSFAC
    tfm              Displays a program's help documentation manual
    tfscan           Scans DNA sequences for transcription factors
    tmap             Displays membrane spanning regions
    topo             Draws an image of a transmembrane protein
    tranalign        Align nucleic coding regions given the aligned proteins
    transeq          Translate nucleic acid sequences
    trimest          Trim poly-A tails off EST sequences
    trimseq          Trim ambiguous bits off the ends of sequences
    twofeat          Finds neighbouring pairs of features in sequences
    union            Reads sequence fragments and builds one sequence
    vectorstrip      Strips out DNA between a pair of vector 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
    water            Smith-Waterman local alignment
    whichdb          Search all databases for an entry
    wobble           Wobble base plot
    wordcount        Counts words of a specified size in a DNA sequence
    wordfinder       Match large sequences against one or more other sequences
    wordmatch        Finds all exact matches of a given size between 2 sequences
    wossname         Finds programs by keywords in their one-line documentation
    yank             Reads a sequence range, appends the 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 one-line documentation

    ACD
    ALIGNMENT CONSENSUS
    ALIGNMENT DIFFERENCES
    ALIGNMENT DOT PLOTS
    ALIGNMENT GLOBAL
    ALIGNMENT LOCAL
    ALIGNMENT MULTIPLE
    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 one-line documentation

       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 standard output
       -filter             boolean    Read standard input, write 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 nameDescription
        acdc ACD compiler
        acdpretty ACD pretty
       printing utility   acdtable Creates an HTML table from
       an ACD file   acdtrace ACD compiler on-screen
       trace   acdvalid
       ACD file validation   ALIGNMENT CONSENSUS  Program nameDescription
        cons Creates a consensus
       from multiple alignments   megamerger Merge two large
       overlapping nucleic acid sequences   merger Merge two overlapping
       sequences   ALIGNMENT DIFFERENCES  [Part of this file has been deleted
       for brevity] Program nameDescription
       dbiblast Index a BLAST
       database   dbifasta
       Database indexing for fasta file databases   dbiflat Index a flat file
       database   dbigcg
       Index a GCG formatted database   dbxfasta Database b+tree indexing
       for fasta file databases   dbxflat Database b+tree indexing for
       flat file databases   dbxgcg Database b+tree indexing for
       GCG formatted databases   UTILS MISC  Program nameDescription
        embossdata Finds or
       fetches data files read by EMBOSS programs   embossversion Writes 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

       If a program's ACD file does not assign the program to a group, it
       will be automatically assigned to the group 'ASSORTED'.

       A program can belong to more than one group.

       The name of this program comes from its use as a favorite word of the
       author Terry Pratchett. It is used especially by the characters of the
       parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.

    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    Information on a multiple sequence alignment
       infoseq      Displays some simple information about sequences
       seealso      Finds programs sharing group names
       showdb       Displays information on the currently available databases
       textsearch   Search sequence documentation. Slow, use SRS and Entrez!
       tfm          Displays a program's help documentation manual
       whichdb      Search all databases for an entry

    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 standard output
       -filter             boolean    Read standard input, write 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

None.

## 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 | Information on a multiple sequence alignment
infoseq | Displays some simple information about sequences
seealso | Finds programs sharing group names
showdb | Displays information on the currently available databases
textsearch | Search sequence documentation. Slow, use SRS and Entrez!
whichdb | Search all databases for an entry
wossname | Finds programs by keywords in their one-line documentation

## 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