| tfm

# Program 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 is primarily held as HTML pages at http://www.uk.embnet.org/Software/EMBOSS/Apps/

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

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 proess 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.

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!

## Usage

Here is a sample session with tfm

    % tfm wossname
    Displays a program's help documentation manual

    ::::::::::::::
    /packages/emboss_dev/gwilliam/emboss/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'
    recoder          Remove restriction sites but maintain the same translation
    remap            Display a sequence with restriction cut sites, translation etc
    restover         Finds restriction enzymes that produce a 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

    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          Displays a 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
    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      Does an all-against-all comparison of a set of sequences
    supermatcher     Finds a match of a large sequence against one or more sequence
    s
    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
    plotcon          Plots the 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 a sequence with restriction cut 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 text. SRS and Entrez are faster!

    EDIT
    biosed           Replace or delete sequence sections
    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
    extractfeat      Extract features from a sequence
    extractseq       Extract regions from a sequence
    listor           Writes 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           Excludes a set of sequences and writes 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 the 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 by a Hanes/Woolf plot

    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

    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 text. SRS and Entrez are faster!
    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

    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          Counts the 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 the 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        Searches 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 the same translation
    redata           Search REBASE for enzyme name, references, suppliers etc
    remap            Display a sequence with restriction cut sites, translation etc
    restover         Finds restriction enzymes that produce a 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 a sequence with restriction cut 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
    distmat          Creates a distance matrix from multiple alignments

    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

    PROTEIN COMPOSITION
    backtranseq      Back translate a protein sequence
    charge           Protein charge plot
    checktrans       Reports STOP codons and ORF statistics of a protein
    compseq          Counts the 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
    fuzzpro          Protein pattern search
    fuzztran         Protein pattern search after translation
    helixturnhelix   Report nucleic acid binding motifs
    oddcomp          Finds 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
    pestfind         Finds PEST motifs as potential proteolytic cleavage sites
    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

    UTILS DATABASE CREATION
    aaindexextract   Extract data from AAINDEX
    cutgextract      Extract data from CUTG
    printsextract    Extract data from PRINTS
    prosextract      Builds the PROSITE motif database for patmatmotifs to search
    rebaseextract    Extract data from REBASE
    tfextract        Extract data from TRANSFAC

    UTILS DATABASE INDEXING
    dbiblast         Index a BLAST database
    dbifasta         Index a fasta database
    dbiflat          Index a flat file database
    dbigcg           Index a GCG formatted database

    UTILS MISC
    embossdata       Finds or fetches the data files read in by the 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
    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
    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
    coderet          Extract CDS, mRNA and translations from feature tables
    compseq          Counts the composition of dimer/trimer/etc words in a sequence
    cons             Creates a consensus from multiple alignments
    cpgplot          Plot CpG rich areas
    cpgreport        Reports all CpG rich regions
    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         Index a fasta database
    dbiflat          Index a flat file database
    dbigcg           Index a GCG formatted database
    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
    dotmatcher       Displays a thresholded dotplot of two sequences
    dotpath          Displays a non-overlapping wordmatch dotplot of two sequences
    dottup           Displays a wordmatch dotplot of two sequences
    dreg             regular expression search of a nucleotide sequence
    einverted        Finds DNA inverted repeats
    embossdata       Finds or fetches the data files read in by the EMBOSS programs
    embossversion    Writes the current EMBOSS version number
    emma             Multiple alignment program - interface to ClustalW program
    emowse           Protein identification by mass spectrometry
    entret           Reads and writes (returns) flatfile entries
    eprimer3         Picks PCR primers and hybridization oligos
    equicktandem     Finds tandem repeats
    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
    findkm           Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot
    freak            Residue/base frequency table or plot
    fuzznuc          Nucleic acid pattern search
    fuzzpro          Protein pattern search
    fuzztran         Protein pattern search after translation
    garnier          Predicts protein secondary structure
    geecee           Calculates the fractional GC content of nucleic acid sequences
    getorf           Finds and extracts open reading frames (ORFs)
    helixturnhelix   Report nucleic acid binding motifs
    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
    isochore         Plots isochores in large DNA sequences
    lindna           Draws linear maps of DNA constructs
    listor           Writes 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
    megamerger       Merge two large overlapping nucleic acid sequences
    merger           Merge two overlapping nucleic acid sequences
    msbar            Mutate sequence beyond all recognition
    mwcontam         Shows molwts that match across a set of files
    mwfilter         Filter noisy molwts from mass spec output
    needle           Needleman-Wunsch global alignment
    needle           Protein global alignment against DNA
    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           Excludes a set of sequences and writes out the remaining ones
    nthseq           Writes one sequence from a multiple set of sequences
    octanol          Displays protein hydropathy
    oddcomp          Finds 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
    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
    pestfind         Finds PEST motifs as potential proteolytic cleavage sites
    plotcon          Plots the 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      Builds the PROSITE motif database for patmatmotifs to search
    pscan            Scans proteins using PRINTS
    rebaseextract    Extract data from REBASE
    recoder          Remove restriction sites but maintain the same translation
    redata           Search REBASE for enzyme name, references, suppliers etc
    remap            Display a sequence with restriction cut sites, translation etc
    restover         Finds restriction enzymes that produce a specific overhang
    restrict         Finds restriction enzyme cleavage sites
    revseq           Reverse and complement a sequence
    seealso          Finds programs sharing group names
    seqmatchall      Does an all-against-all comparison of a set of sequences
    seqret           Reads and writes (returns) sequences
    seqretsplit      Reads and writes (returns) sequences in individual files
    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
    silent           Silent mutation restriction enzyme scan
    sirna            Finds siRNA duplexes in mRNA
    sixpack          Display a DNA sequence with 6-frame translation and ORFs
    skipseq          Reads and writes (returns) sequences, skipping the first few
    splitter         Split a sequence into (overlapping) smaller sequences
    stretcher        Finds the best global alignment between two sequences
    stssearch        Searches a DNA database for matches with a set of STS primers
    supermatcher     Finds a match of a large sequence against one or more sequence
    s
    syco             Synonymous codon usage Gribskov statistic plot
    tcode            Fickett TESTCODE statistic to identify protein-coding DNA
    textsearch       Search sequence documentation text. SRS and Entrez are faster!
    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
    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

    ALIGNMENT CONSENSUS
    ALIGNMENT DIFFERENCES
    ALIGNMENT DOT PLOTS
    ALIGNMENT GLOBAL
    ALIGNMENT LOCAL
    ALIGNMENT MULTIPLE
    DISPLAY
    EDIT
    ENZYME KINETICS
    FEATURE TABLES
    INFORMATION
    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
    PROTEIN 2D STRUCTURE
    PROTEIN COMPOSITION
    PROTEIN MOTIFS
    PROTEIN MUTATION
    PROTEIN PROFILES
    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:

         * ALIGNMENT CONSENSUS
         * ALIGNMENT DIFFERENCES
         * ALIGNMENT DOT PLOTS
         * ALIGNMENT GLOBAL
         * ALIGNMENT LOCAL
         * ALIGNMENT MULTIPLE
         * DISPLAY
         * EDIT
         * ENZYME KINETICS
         * FEATURE TABLES
         * INFORMATION
         * 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
         * PROTEIN 2D STRUCTURE
         * PROTEIN COMPOSITION
         * PROTEIN MOTIFS
         * PROTEIN MUTATION
         * PROTEIN PROFILES
         * UTILS DATABASE CREATION
         * UTILS DATABASE INDEXING
         * UTILS MISC

       Example 6

       Output html tags around the list of programs:

    % wossname '' -html -prelink 'http://www.uk.embnet.org/Software/EMBOSS/Apps/' -
    postlink '.html' -out wossname.html
    Finds programs by keywords in their one-line documentation

       Go to the output files for this example

    Command line arguments

       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.

       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    If you enter the name of a file here then
                                      this program will write the program names
                                      and brief descriptions into that file.
       -html               boolean    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 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 sheme, ie. they
                                      may wish to charge money for them.
       -[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 sheme, ie. they
                                      may wish to charge money for them.
       -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" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

       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
       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 If you enter the name of a file here then this program will
       write the program names and brief descriptions into that file. 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. Boolean 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 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 sheme, ie. they may wish to charge money for them.
       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 sheme, ie. they may wish to charge money for them.
       Boolean value Yes/No Yes
       -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

    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      Displays a 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
       est2genome   Align EST and genomic DNA sequences
       needle       Needleman-Wunsch global alignment
       stretcher    Finds the best global alignment between two sequences

    ALIGNMENT LOCAL

       Program name Description
       matcher Finds the best local alignments between two sequences
       seqmatchall Does an all-against-all comparison of a set of sequences
       supermatcher Finds a match of a large sequence against one or more
       sequences
       water Smith-Waterman local alignment
       wordmatch Finds all exact matches of a given size between 2 sequences

    ALIGNMENT MULTIPLE

       Program name                        Description
       emma         Multiple alignment program - interface to ClustalW program
       infoalign    Information on a multiple sequence alignment
       plotcon      Plots the 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

        Program name                         Description
       abiview        Reads ABI file and display the trace
       [Part of this file has been deleted for brevity]
       antigenic      Finds antigenic sites in proteins
       digest         Protein proteolytic enzyme or reagent cleavage digest
       fuzzpro        Protein pattern search
       fuzztran       Protein pattern search after translation
       helixturnhelix Report nucleic acid binding motifs
       oddcomp        Finds 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
       pestfind       Finds PEST motifs as potential proteolytic cleavage sites
       preg           Regular expression search of a protein sequence
       pscan          Scans proteins using PRINTS
       sigcleave      Reports protein signal cleavage sites

    PROTEIN MUTATION

       Program name                     Description
       msbar        Mutate sequence beyond all recognition
       shuffleseq   Shuffles a set of sequences maintaining composition

    PROTEIN PROFILES

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

    UTILS DATABASE CREATION

       Program name Description
       aaindexextract Extract data from AAINDEX
       cutgextract Extract data from CUTG
       printsextract Extract data from PRINTS
       prosextract Builds the PROSITE motif database for patmatmotifs to
       search
       rebaseextract Extract data from REBASE
       tfextract Extract data from TRANSFAC

    UTILS DATABASE INDEXING

       Program name          Description
       dbiblast     Index a BLAST database
       dbifasta     Index a fasta database
       dbiflat      Index a flat file database
       dbigcg       Index a GCG formatted database

    UTILS MISC

       Program name Description
       embossdata Finds or fetches the data files read in by the 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 text. SRS and Entrez are
       faster!
       tfm Displays a program's help documentation manual
       whichdb Search all databases for an entry

    Author(s)

       Gary Williams (gwilliam © hgmp.mrc.ac.uk)
       HGMP-RC, 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

## Command line arguments

       Mandatory qualifiers:
      [-program]           string     Enter the name of an EMBOSS program

       Optional qualifiers:
       -outfile            outfile    If you enter the name of a file here then
                                      this program will write the program names
                                      and brief descriptions into that file.
       -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 qualifiers: (none)
       Associated qualifiers:
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-program] (Parameter 1) | Enter the name of an EMBOSS program | A string of at least 1 characters | Required
Optional qualifiers | Allowed values | Default
-outfile | If you enter the name of a file here then this program will write the program names and brief descriptions into that 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 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://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/

## 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 text. SRS and Entrez are faster!
whichdb | Search all databases for an entry
wossname | Finds programs by keywords in their one-line documentation

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, 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