| 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@embnet.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

    % tfm wossname
    Displays a program's help documentation manual

                                     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
    remap            Display sequence with restriction sites, translation etc
    restover         Find restriction enzymes producing specific overhang
    restrict         Finds restriction enzyme cleavage sites
    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 nucleic acid 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
    alignrunner      Align sequence pairs in a directory
    comparator       Compare contact scores of two sequence alignments
    contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
    esim4            Align an mRNA to a genomic DNA sequence
    est2genome       Align EST and genomic DNA sequences
    nawalign         Damian Counsell's NW implementation
    nawalignrunner   Nawalign all sequence pairs in a directory
    needle           Needleman-Wunsch global alignment
    needlerunner     Needle all sequence pairs in a directory
    scorer           Score alignments using structural alignments
    scorerrunner     SCORER for ordered pairs of substituted seqs
    stretcher        Finds the best global alignment between two sequences
    substitute       Substitute matches into a template
    substituterunner Run SUBSTITUTE on a directory of traces

    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
    wordmatch        Finds all exact matches of a given size between 2 sequences

    ALIGNMENT MULTIPLE
    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
    degapseqrunner   Degapseq all sequence pairs in a directory
    descseq          Alter the name or description of a sequence
    entret           Reads and writes (returns) flatfile entries
    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
    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
    ealistat         Statistics for multiple alignment files
    ehmmalign        Align sequences with an HMM
    ehmmbuild        Build HMM
    ehmmcalibrate    Calibrate a hidden Markov model
    ehmmconvert      Convert between HMM formats
    ehmmemit         Extract HMM sequences
    ehmmfetch        Extract HMM from a database
    ehmmindex        Index an HMM database
    ehmmpfam         Align single sequence with an HMM
    ehmmsearch       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

    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 TRANSCRIPTION
    tfscan           Scans DNA sequences for transcription factors

    NUCLEIC TRANSLATION
    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
    distmat          Creates a distance matrix from multiple alignments
    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
    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 pasimony 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
    contactcount     Count specific versus non-specific contacts
    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
    scorecmapdir     Contact scores for cleaned protein chain contact 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
    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
    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
    meme             Motif detection
    oddcomp          Find protein sequence regions with a biased composition
    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

    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
    alignrunner      Align sequence pairs in a directory
    allversusall     Sequence similarity data from all-versus-all comparison
    antigenic        Finds antigenic sites in proteins
    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
    comparator       Compare contact scores of two sequence alignments
    compseq          Count composition of dimer/trimer/etc words in a sequence
    cons             Creates a consensus from multiple alignments
    contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
    contactcount     Count specific versus non-specific contacts
    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
    degapseqrunner   Degapseq all sequence pairs in a directory
    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
    ealistat         Statistics for multiple alignment files
    eclique          Largest clique program
    econsense        Majority-rule and strict consensus tree
    econtml          Continuous character Maximum Likelihood method
    econtrast        Continuous character Contrasts
    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 with an HMM
    ehmmbuild        Build HMM
    ehmmcalibrate    Calibrate a hidden Markov model
    ehmmconvert      Convert between HMM formats
    ehmmemit         Extract HMM sequences
    ehmmfetch        Extract HMM from a database
    ehmmindex        Index an HMM database
    ehmmpfam         Align single sequence with an HMM
    ehmmsearch       Search sequence database with an HMM
    einverted        Finds DNA inverted repeats
    ekitsch          Fitch-Margoliash method with contemporary tips
    embossdata       Finds or fetches data files read by EMBOSS programs
    embossversion    Writes the current EMBOSS version number
    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
    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 pasimony 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
    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
    meme             Motif detection
    merger           Merge two overlapping nucleic acid 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
    nawalign         Damian Counsell's NW implementation
    nawalignrunner   Nawalign all sequence pairs in a directory
    needle           Needleman-Wunsch global alignment
    needlerunner     Needle all sequence pairs in a directory
    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
    octanol          Displays protein hydropathy
    oddcomp          Find protein sequence regions with a biased composition
    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
    scorecmapdir     Contact scores for cleaned protein chain contact files
    scorer           Score alignments using structural alignments
    scorerrunner     SCORER for ordered pairs of substituted seqs
    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
    substitute       Substitute matches into a template
    substituterunner Run SUBSTITUTE on a directory of traces
    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
    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
    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 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 program groups:

    % wossname -groups -html -prelink '#'
    Finds programs by keywords in their one-line documentation
    Keyword to search for, or blank to list all programs:

         * 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 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 6

       Output html tags around the list of programs:

    % wossname '' -html -prelink 'http://emboss.sf.net/apps/' -postlink '.html' -ou
    t 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 of all of the
                                      EMBOSS programs. If no keyword is specified,
                                      all programs will be listed.

       Additional (Optional) qualifiers (* if not always prompted):
       -explode            boolean    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'.
       -outfile            outfile    Output file name
       -html               toggle     If you are sending the output to a file,
                                      this will format it for displaying as a
                                      table in a WWW document.
    *  -prelink            string     If you are outputting to a file in HTML
                                      format, you can make the program names into
                                      hyper-links by setting this to be the first
                                      half of the URL.
                                      For example, if you wish the program name to
                                      be a hyperlink to the URL:
                                      http://www.uk.embnet.org/Software/EMBOSS/Apps
    /programname.html
                                      then if you enter
                                      http://www.uk.embnet.org/Software/EMBOSS/Apps
    /
                                      here, then the first half of the URL before
                                      the programname will be set.
    *  -postlink           string     If you are outputting to a file in HTML
                                      format, you can make the program names into
                                      hyper-links by setting this to be the second
                                      half of the URL.
                                      For example, if you wish the program name to
                                      be a hyperlink to the URL:
                                      http://www.uk.embnet.org/Software/EMBOSS/Apps
    /programname.html
                                      then if you enter '.html' here, the second
                                      half of the URL after the programname will
                                      be set.
       -groups             boolean    If you use this option, then only the group
                                      names will output to the file
       -alphabetic         boolean    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    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    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
       -colon              boolean    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    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 deaths

       Standard (Mandatory) qualifiers Allowed values Default
       [-search]
       (Parameter 1) Enter a word or words here and a case-independent search
       for it will be made in the one-line documentation of all of the EMBOSS
       programs. If no keyword is specified, all programs will be listed. Any
       string is accepted An empty string is accepted
       Additional (Optional) qualifiers Allowed values Default
       -explode 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'. Boolean value
       Yes/No No
       -outfile Output file name Output file stdout
       -html If you are sending the output to a file, this will format it for
       displaying as a table in a WWW document. Toggle value Yes/No No
       -prelink If you are outputting to a file in HTML format, you can make
       the program names into hyper-links by setting this to be the first
       half of the URL. For example, if you wish the program name to be a
       hyperlink to the URL:
       http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if
       you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then
       the first half of the URL before the programname will be set. Any
       string is accepted An empty string is accepted
       -postlink If you are outputting to a file in HTML format, you can make
       the program names into hyper-links by setting this to be the second
       half of the URL. For example, if you wish the program name to be a
       hyperlink to the URL:
       http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if
       you enter '.html' here, the second half of the URL after the
       programname will be set. Any string is accepted An empty string is
       accepted
       -groups If you use this option, then only the group names will output
       to the file Boolean value Yes/No No
       -alphabetic 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. Boolean value Yes/No No
       Advanced (Unprompted) qualifiers Allowed values Default
       -[no]emboss 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 Boolean value Yes/No Yes
       -[no]embassy 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 Boolean value Yes/No Yes
       -showembassy 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 An
       empty string is accepted
       -colon 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. Boolean value Yes/No No
       -gui 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 Boolean value Yes/No No

    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 6

      File: wossname.html

    ACD

       Program name              Description
       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 name                    Description
       cons         Creates a consensus from multiple alignments
       megamerger   Merge two large overlapping nucleic acid sequences
       merger       Merge two overlapping nucleic acid sequences

    ALIGNMENT DIFFERENCES

       Program name                     Description
       diffseq      Find differences between nearly identical sequences

    ALIGNMENT DOT PLOTS

       Program name                       Description
       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

         Program name                         Description
       alignrunner      Align sequence pairs in a directory
       comparator       Compare contact scores of two sequence alignments
       contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
       esim4            Align an mRNA to a genomic DNA sequence
       est2genome       Align EST and genomic DNA sequences
       nawalign         Damian Counsell's NW implementation
       nawalignrunner   Nawalign all sequence pairs in a directory
       needle           Needleman-Wunsch global alignment
       needlerunner     Needle all sequence pairs in a directory
       scorer           Score alignments using structural alignments
       scorerrunner     SCORER for ordered pairs of substituted seqs
       stretcher        Finds the best global alignment between two sequences
       substitute       Substitute matches into a template
       substituterunner Run SUBSTITUTE on a directory of traces

    ALIGNMENT LOCAL

       Program name                     Description
       [Part of this file has been deleted for brevity]
       profit       Scan a sequence or database with a matrix or profile
       prophecy     Creates matrices/profiles from multiple alignments
       prophet      Gapped alignment for profiles

    TEST

       Program name                      Description
       crystalball  Answers every drug discovery question about a sequence
       myseq        Demonstration of sequence reading

    UTILS DATABASE CREATION

        Program name                        Description
       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

       Program name                     Description
       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 name                      Description
       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

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

       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 deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-program] (Parameter 1) | Enter the name of an EMBOSS program | A string of at least 1 characters | Required
Additional (Optional) qualifiers | Allowed values | Default
-outfile | Output file name | 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