EMBOSS

| tfm

## Wiki

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

Please help by correcting and extending the Wiki pages.

## Function

Display full documentation for an application

## Description

tfm displays help information for the specified EMBOSS program.

## Usage

Here is a sample session with tfm

##

##

##

    % tfm wossname
    Display full documentation for an application

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

    Wiki

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

       Please help by correcting and extending the Wiki pages.

    Function

       Find programs by keywords in their short description

    Description

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

    Usage

       Here is a sample session with wossname

       Search for programs with 'restrict' in their description:

    % wossname restrict
    Find programs by keywords in their short description

    SEARCH FOR 'RESTRICT'
    erestml       Restriction site maximum likelihood method
    frestboot     Bootstrapped restriction sites algorithm
    frestdist     Calculate distance matrix from restriction sites or fragments
    frestml       Restriction site maximum likelihood method
    rebaseextract Process the REBASE database for use by restriction enzyme applicat
    ions
    recoder       Find restriction sites to remove (mutate) with no translation chan
    ge
    redata        Retrieve information from REBASE restriction enzyme database
    remap         Display restriction enzyme binding sites in a nucleotide sequence
    restover      Find restriction enzymes producing a specific overhang
    restrict      Report restriction enzyme cleavage sites in a nucleotide sequence
    showseq       Display sequences with features in pretty format
    silent        Find restriction sites to insert (mutate) with no translation chan
    ge

       Example 2

       Display a listing of programs in their groups:

    % wossname -search ""
    Find programs by keywords in their short description

    ACD
    acdc      Test an application ACD file
    acdpretty Correctly reformat an application ACD file
    acdtable  Generate an HTML table of parameters from an application ACD file
    acdtrace  Trace processing of an application ACD file (for testing)
    acdvalid  Validate an application ACD file

    ALIGNMENT
    extractalign Extract regions from a sequence alignment

    ALIGNMENT CONSENSUS
    cons       Create a consensus sequence from a multiple alignment
    consambig  Create an ambiguous consensus sequence from a multiple alignment
    megamerger Merge two large overlapping DNA sequences
    merger     Merge two overlapping sequences

    ALIGNMENT DIFFERENCES
    diffseq Compare and report features of two similar sequences

    ALIGNMENT DOT PLOTS
    dotmatcher Draw a threshold dotplot of two sequences
    dotpath    Draw a non-overlapping wordmatch dotplot of two sequences
    dottup     Display a wordmatch dotplot of two sequences
    polydot    Draw dotplots for all-against-all comparison of a sequence set

    ALIGNMENT GLOBAL
    esim4      Align an mRNA to a genomic DNA sequence
    est2genome Align EST sequences to genomic DNA sequence
    needle     Needleman-Wunsch global alignment of two sequences
    needleall  Many-to-many pairwise alignments of two sequence sets
    stretcher  Needleman-Wunsch rapid global alignment of two sequences

    ALIGNMENT LOCAL
    domainalign  Generate alignments (DAF file) for nodes in a DCF file
    domainrep    Reorder DCF file to identify representative structures
    matcher      Waterman-Eggert local alignment of two sequences
    oalistat     Statistics for multiple alignment files
    seqalign     Extend alignments (DAF file) with sequences (DHF file)
    seqmatchall  All-against-all word comparison of a sequence set
    supermatcher Calculate approximate local pair-wise alignments of larger sequence
    s
    water        Smith-Waterman local alignment of sequences
    wordfinder   Match large sequences against one or more other sequences
    wordmatch    Find regions of identity (exact matches) of two sequences

    ALIGNMENT MULTIPLE
    edialign   Local multiple alignment of sequences
    emma       Multiple sequence alignment (ClustalW wrapper)
    eomega     Multiple sequence alignment (ClustalO wrapper)
    eomegapp   Profile with profile (ClustalO wrapper)
    eomegash   Sequence with HMM (ClustalO wrapper)
    eomegasp   Sequence with profile (ClustalO wrapper)
    infoalign  Display basic information about a multiple sequence alignment
    mse        Multiple sequence editor
    plotcon    Plot conservation of a sequence alignment
    prettyplot Draw a sequence alignment with pretty formatting
    showalign  Display a multiple sequence alignment in pretty format
    tranalign  Generate an alignment of nucleic coding regions from aligned proteins

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

    DATA RESOURCES
    cachedas         Generate server cache file for DAS servers or for the DAS regis
    try
    cachedbfetch     Generate server cache file for Dbfetch/WSDbfetch data sources
    cacheebeyesearch Generate server cache file for EB-eye search domains
    cacheensembl     Generate server cache file for an Ensembl server
    dbtell           Display information about a public database
    servertell       Display information about a public server
    showdb           Display information on configured databases
    showserver       Display information on configured servers

    DATA RETRIEVAL
    codcopy Copy and reformat a codon usage table
    seqret  Read and write (return) sequences

    DATA RETRIEVAL CHEMISTRY DATA
    infobase    Return information on a given nucleotide base
    inforesidue Return information on a given amino acid residue

    DATA RETRIEVAL FEATURE DATA
    featcopy  Read and write a feature table
    featmerge Merge two overlapping feature tables

    DATA RETRIEVAL ONTOLOGY DATA
    edamdef         Find EDAM ontology terms by definition
    edamhasinput    Find EDAM ontology terms by has_input relation
    edamhasoutput   Find EDAM ontology terms by has_output relation
    edamisformat    Find EDAM ontology terms by is_format_of relation
    edamisid        Find EDAM ontology terms by is_identifier_of relation
    edamname        Find EDAM ontology terms by name
    godef           Find GO ontology terms by definition
    goname          Find GO ontology terms by name
    ontoget         Get ontology term(s)
    ontogetcommon   Get common ancestor for terms
    ontogetdown     Get ontology term(s) by parent id
    ontogetobsolete Get ontology ontology terms
    ontogetroot     Get ontology root terms by child identifier
    ontogetsibs     Get ontology term(s) by id with common parent
    ontogetup       Get ontology term(s) by id of child
    ontoisobsolete  Report whether an ontology term id is obsolete
    ontotext        Get ontology term(s) original full text

    DATA RETRIEVAL RESOURCE DATA
    drfinddata     Find public databases by data type
    drfindformat   Find public databases by format
    drfindid       Find public databases by identifier
    drfindresource Find public databases by resource
    drget          Get data resource entries
    drtext         Get data resource entries complete text

    DATA RETRIEVAL SEQUENCE DATA
    abiview      Display the trace in an ABI sequencer file
    coderet      Extract CDS, mRNA and translations from feature tables
    entret       Retrieve sequence entries from flatfile databases and files
    extractalign Extract regions from a sequence alignment
    infoalign    Display basic information about a multiple sequence alignment
    infoseq      Display basic information about sequences
    refseqget    Get reference sequence
    seqxref      Retrieve all database cross-references for a sequence entry
    seqxrefget   Retrieve all cross-referenced data for a sequence entry
    showalign    Display a multiple sequence alignment in pretty format
    variationget Get sequence variations
    whichdb      Search all sequence databases for an entry and retrieve it

    DATA RETRIEVAL SEQUENCE DATA ASSEMBLY DATA
    assemblyget  Get assembly of sequence reads
    infoassembly Display information about assemblies

    DATA RETRIEVAL TEXT DATA
    drtext     Get data resource entries complete text
    entret     Retrieve sequence entries from flatfile databases and files
    ontotext   Get ontology term(s) original full text
    textget    Get text data entries
    textsearch Search the textual description of sequence(s)

    DATA RETRIEVAL TOOL DATA
    acdc      Test an application ACD file
    acdpretty Correctly reformat an application ACD file
    acdtable  Generate an HTML table of parameters from an application ACD file
    acdtrace  Trace processing of an application ACD file (for testing)
    acdvalid  Validate an application ACD file

    DATA RETRIEVAL URL DATA
    urlget Get URLs of data resources

    DISPLAY
    abiview    Display the trace in an ABI sequencer file
    cirdna     Draw circular map of DNA constructs
    iep        Calculate the isoelectric point of proteins
    lindna     Draw linear maps of DNA constructs
    pepinfo    Plot amino acid properties of a protein sequence in parallel
    pepnet     Draw a helical net for a protein sequence
    pepwheel   Draw a helical wheel diagram for a protein sequence
    plotorf    Plot potential open reading frames in a nucleotide sequence
    prettyplot Draw a sequence alignment with pretty formatting
    prettyseq  Write a nucleotide sequence and its translation to file
    remap      Display restriction enzyme binding sites in a nucleotide sequence
    showfeat   Display features of a sequence in pretty format
    showpep    Display protein sequences with features in pretty format
    sixpack    Display a DNA sequence with 6-frame translation and ORFs
    topo       Draw an image of a transmembrane protein

    DOCUMENTATION
    seealso       Find programs with similar function to a specified program
    tfm           Display full documentation for an application
    wossdata      Find programs by EDAM data
    wossinput     Find programs by EDAM input data
    wossname      Find programs by keywords in their short description
    wossoperation Find programs by EDAM operation
    wossoutput    Find programs by EDAM output data
    wossparam     Find programs by EDAM parameter
    wosstopic     Find programs by EDAM topic

    EDIT
    aligncopy     Read and write alignments
    aligncopypair Read and write pairs from alignments
    biosed        Replace or delete sequence sections
    codcopy       Copy and reformat a codon usage table
    cutseq        Remove a section from a sequence
    degapseq      Remove non-alphabetic (e.g. gap) characters from sequences
    descseq       Alter the name or description of a sequence
    entret        Retrieve sequence entries from flatfile databases and files
    extractalign  Extract regions from a sequence alignment
    extractfeat   Extract features from sequence(s)
    extractseq    Extract regions from a sequence
    featcopy      Read and write a feature table
    featmerge     Merge two overlapping feature tables
    featreport    Read and write a feature table
    feattext      Return a feature table original text
    listor        Write a list file of the logical OR of two sets of sequences
    makenucseq    Create random nucleotide sequences
    makeprotseq   Create random protein sequences
    maskambignuc  Mask all ambiguity characters in nucleotide sequences with N
    maskambigprot Mask all ambiguity characters in protein sequences with X
    maskfeat      Write a sequence with masked features
    maskseq       Write a sequence with masked regions
    newseq        Create a sequence file from a typed-in sequence
    nohtml        Remove mark-up (e.g. HTML tags) from an ASCII text file
    noreturn      Remove carriage return from ASCII files
    nospace       Remove whitespace from an ASCII text file
    notab         Replace tabs with spaces in an ASCII text file
    notseq        Write to file a subset of an input stream of sequences
    nthseq        Write to file a single sequence from an input stream of sequences
    nthseqset     Read and write (return) one set of sequences from many
    pasteseq      Insert one sequence into another
    revseq        Reverse and complement a nucleotide sequence
    seqcount      Read and count sequences
    seqfraggle    Remove fragment sequences from DHF files
    seqret        Read and write (return) sequences
    seqretsetall  Read and write (return) many sets of sequences
    seqretsplit   Read sequences and write them to individual files
    sizeseq       Sort sequences by size
    skipredundant Remove redundant sequences from an input set
    skipseq       Read and write (return) sequences, skipping first few
    splitsource   Split sequence(s) into original source sequences
    splitter      Split sequence(s) into smaller sequences
    trimest       Remove poly-A tails from nucleotide sequences
    trimseq       Remove unwanted characters from start and end of sequence(s)
    trimspace     Remove extra whitespace from an ASCII text file
    union         Concatenate multiple sequences into a single sequence
    vectorstrip   Remove vectors from the ends of nucleotide sequence(s)
    yank          Add a sequence reference (a full USA) to a list file

    ENZYME KINETICS
    findkm Calculate and plot enzyme reaction data

    FEATURE TABLES
    extractfeat Extract features from sequence(s)
    maskfeat    Write a sequence with masked features
    showfeat    Display features of a sequence in pretty format
    twofeat     Find neighbouring pairs of features in sequence(s)

    HMM
    ehmmalign     Align sequences to an HMM profile
    ehmmbuild     Build a profile HMM from an alignment
    ehmmcalibrate Calibrate HMM search statistics
    ehmmconvert   Convert between profile HMM file formats
    ehmmemit      Generate sequences from a profile HMM
    ehmmfetch     Retrieve an HMM from an HMM database
    ehmmindex     Create a binary SSI index for an HMM database
    ehmmpfam      Search one or more sequences against an HMM database
    ehmmsearch    Search a sequence database with a profile HMM
    libgen        Generate discriminating elements from alignments
    ohmmalign     Align sequences with an HMM
    ohmmbuild     Build HMM
    ohmmcalibrate Calibrate a hidden Markov model
    ohmmconvert   Convert between HMM formats
    ohmmemit      Extract HMM sequences
    ohmmfetch     Extract HMM from a database
    ohmmindex     Index an HMM database
    ohmmpfam      Align single sequence with an HMM
    ohmmsearch    Search sequence database with an HMM

    MENUS
    emnu   Simple menu of EMBOSS applications

    NUCLEIC 2D STRUCTURE
    banana          Plot bending and curvature data for B-DNA
    btwisted        Calculate the twisting in a B-DNA sequence
    einverted       Find inverted repeats in nucleotide sequences
    ovrnaalifold    Calculate secondary structures for a set of aligned RNAs
    ovrnaalifoldpf  Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    ovrnacofold     Calculate secondary structures of RNA dimers
    ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations)
    ovrnacofoldpf   Calculate secondary structures of RNA dimers (partitioning)
    ovrnadistance   Calculate distances between RNA secondary structures
    ovrnaduplex     Predict RNA duplex (hybridization) sites and structure
    ovrnaeval       Calculate energy of RNA sequences with a given secondary structu
    re
    ovrnaevalpair   Calculate energy of RNA sequences on given secondary structure
    ovrnafold       Calculate min. energy RNA structure / pair probabilities (partit
    ion)
    ovrnafoldpf     Calculate min. energy RNA structure / pair probabilities
    ovrnaheat       Calculate specific heat of RNA melting
    ovrnainverse    Find RNA sequences with a given secondary structure
    ovrnalfold      Calculate locally stable secondary structures of RNAs
    ovrnaplot       Draw RNA secondary structures
    ovrnasubopt     Calculate suboptimal secondary structure of RNA
    sirna           Find siRNA duplexes in mRNA
    vrna2dfold      Calculate RNA structures and samples of k,l neighbourhoods
    vrnaaliduplex   RNA duplex calculation for two sequence alignments
    vrnaalifold     Calculate secondary structures for a set of aligned RNAs
    vrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    vrnacofold      Calculate secondary structures of RNA dimers
    vrnacofoldconc  Calculate secondary structures of RNA dimers (concentrations)
    vrnacofoldpf    Calculate secondary structures of RNA dimers (partitioning)
    vrnadistance    Calculate distances between RNA secondary structures
    vrnaduplex      Predict RNA duplex (hybridization) sites and structure
    vrnaeval        Calculate energy of RNA sequences with a given secondary structu
    re
    vrnaevalpair    Calculate energy of RNA sequences on given secondary structure
    vrnafold        Calculate min. energy RNA secondary structures and pair probabil
    ities
    vrnafoldpf      Calculate min. energy RNA structures / pair probabilities (parti
    tion)
    vrnaheat        Calculate specific heat of RNA melting
    vrnainverse     Find RNA sequences with a given secondary structure
    vrnalalifoldpf  Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    vrnalfold       Calculate locally stable secondary structures of RNAs
    vrnalfoldz      Calculate locally stable secondary structures of RNAs plus zscor
    e
    vrnapkplex      Calculate RNA structures plus pseudoknots
    vrnaplfold      Compute avg. pair probabilities for local base pairs in RNA sequ
    ences
    vrnaplot        Draw RNA secondary structures
    vrnasubopt      Calculate suboptimal secondary structures of RNAs

    NUCLEIC CODON USAGE
    cai     Calculate codon adaptation index
    chips   Calculate Nc codon usage statistic
    codcmp  Codon usage table comparison
    codcopy Copy and reformat a codon usage table
    cusp    Create a codon usage table from nucleotide sequence(s)
    syco    Draw synonymous codon usage statistic plot for a nucleotide sequence

    NUCLEIC COMPOSITION
    banana    Plot bending and curvature data for B-DNA
    btwisted  Calculate the twisting in a B-DNA sequence
    chaos     Draw a chaos game representation plot for a nucleotide sequence
    compseq   Calculate the composition of unique words in sequences
    dan       Calculate nucleic acid melting temperature
    density   Draw a nucleic acid density plot
    freak     Generate residue/base frequency table or plot
    isochore  Plot isochores in DNA sequences
    wordcount Count and extract unique words in molecular sequence(s)

    NUCLEIC CPG ISLANDS
    cpgplot      Identify and plot CpG islands in nucleotide sequence(s)
    cpgreport    Identify and report CpG-rich regions in nucleotide sequence(s)
    geecee       Calculate fractional GC content of nucleic acid sequences
    newcpgreport Identify CpG islands in nucleotide sequence(s)
    newcpgseek   Identify and report CpG-rich regions in nucleotide sequence(s)

    NUCLEIC FUNCTIONAL SITES
    marscan Find matrix/scaffold recognition (MRS) signatures in DNA sequences
    sirna   Find siRNA duplexes in mRNA
    trimest Remove poly-A tails from nucleotide sequences

    NUCLEIC GENE FINDING
    checktrans Report STOP codons and ORF statistics of a protein
    getorf     Find and extract open reading frames (ORFs)
    marscan    Find matrix/scaffold recognition (MRS) signatures in DNA sequences
    plotorf    Plot potential open reading frames in a nucleotide sequence
    showorf    Display a nucleotide sequence and translation in pretty format
    sixpack    Display a DNA sequence with 6-frame translation and ORFs
    syco       Draw synonymous codon usage statistic plot for a nucleotide sequence
    tcode      Identify protein-coding regions using Fickett TESTCODE statistic
    wobble     Plot third base position variability in a nucleotide sequence

    NUCLEIC MOTIFS
    dreg     Regular expression search of nucleotide sequence(s)
    fuzznuc  Search for patterns in nucleotide sequences
    fuzztran Search for patterns in protein sequences (translated)

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

    NUCLEIC PRIMERS
    eprimer3     Pick PCR primers and hybridization oligos
    eprimer32    Pick PCR primers and hybridization oligos
    primersearch Search DNA sequences for matches with primer pairs
    stssearch    Search a DNA database for matches with a set of STS primers

    NUCLEIC PROFILES
    profit   Scan one or more sequences with a simple frequency matrix
    prophecy Create frequency matrix or profile from a multiple alignment
    prophet  Scan one or more sequences with a Gribskov or Henikoff profile

    NUCLEIC PROPERTIES
    banana   Plot bending and curvature data for B-DNA
    btwisted Calculate the twisting in a B-DNA sequence
    dan      Calculate nucleic acid melting temperature
    vrnaheat Calculate specific heat of RNA melting

    NUCLEIC REPEATS
    einverted    Find inverted repeats in nucleotide sequences
    equicktandem Find tandem repeats in nucleotide sequences
    etandem      Find tandem repeats in a nucleotide sequence
    palindrome   Find inverted repeats in nucleotide sequence(s)

    NUCLEIC RESTRICTION
    recoder  Find restriction sites to remove (mutate) with no translation change
    redata   Retrieve information from REBASE restriction enzyme database
    remap    Display restriction enzyme binding sites in a nucleotide sequence
    restover Find restriction enzymes producing a specific overhang
    restrict Report restriction enzyme cleavage sites in a nucleotide sequence
    showseq  Display sequences with features in pretty format
    silent   Find restriction sites to insert (mutate) with no translation change

    NUCLEIC RNA FOLDING
    ovrnaalifold    Calculate secondary structures for a set of aligned RNAs
    ovrnaalifoldpf  Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    ovrnacofold     Calculate secondary structures of RNA dimers
    ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations)
    ovrnacofoldpf   Calculate secondary structures of RNA dimers (partitioning)
    ovrnadistance   Calculate distances between RNA secondary structures
    ovrnaduplex     Predict RNA duplex (hybridization) sites and structure
    ovrnaeval       Calculate energy of RNA sequences with a given secondary structu
    re
    ovrnaevalpair   Calculate energy of RNA sequences on given secondary structure
    ovrnafold       Calculate min. energy RNA structure / pair probabilities (partit
    ion)
    ovrnafoldpf     Calculate min. energy RNA structure / pair probabilities
    ovrnaheat       Calculate specific heat of RNA melting
    ovrnainverse    Find RNA sequences with a given secondary structure
    ovrnalfold      Calculate locally stable secondary structures of RNAs
    ovrnaplot       Draw RNA secondary structures
    ovrnasubopt     Calculate suboptimal secondary structure of RNA
    vrna2dfold      Calculate RNA structures and samples of k,l neighbourhoods
    vrnaaliduplex   RNA duplex calculation for two sequence alignments
    vrnaalifold     Calculate secondary structures for a set of aligned RNAs
    vrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    vrnacofold      Calculate secondary structures of RNA dimers
    vrnacofoldconc  Calculate secondary structures of RNA dimers (concentrations)
    vrnacofoldpf    Calculate secondary structures of RNA dimers (partitioning)
    vrnadistance    Calculate distances between RNA secondary structures
    vrnaduplex      Predict RNA duplex (hybridization) sites and structure
    vrnaeval        Calculate energy of RNA sequences with a given secondary structu
    re
    vrnaevalpair    Calculate energy of RNA sequences on given secondary structure
    vrnafold        Calculate min. energy RNA secondary structures and pair probabil
    ities
    vrnafoldpf      Calculate min. energy RNA structures / pair probabilities (parti
    tion)
    vrnaheat        Calculate specific heat of RNA melting
    vrnainverse     Find RNA sequences with a given secondary structure
    vrnalalifoldpf  Calculate secondary structures for a set of aligned RNAs (partit
    ion)
    vrnalfold       Calculate locally stable secondary structures of RNAs
    vrnalfoldz      Calculate locally stable secondary structures of RNAs plus zscor
    e
    vrnapkplex      Calculate RNA structures plus pseudoknots
    vrnaplfold      Compute avg. pair probabilities for local base pairs in RNA sequ
    ences
    vrnaplot        Draw RNA secondary structures
    vrnasubopt      Calculate suboptimal secondary structures of RNAs

    NUCLEIC TRANSCRIPTION
    jaspscan Scan DNA sequences for transcription factors
    marscan  Find matrix/scaffold recognition (MRS) signatures in DNA sequences
    tfscan   Identify transcription factor binding sites in DNA sequences

    NUCLEIC TRANSLATION
    backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
    backtranseq   Back-translate a protein sequence to a nucleotide sequence
    checktrans    Report STOP codons and ORF statistics of a protein
    coderet       Extract CDS, mRNA and translations from feature tables
    plotorf       Plot potential open reading frames in a nucleotide sequence
    prettyseq     Write a nucleotide sequence and its translation to file
    remap         Display restriction enzyme binding sites in a nucleotide sequence
    showorf       Display a nucleotide sequence and translation in pretty format
    showseq       Display sequences with features in pretty format
    sixpack       Display a DNA sequence with 6-frame translation and ORFs
    transeq       Translate nucleic acid sequences

    ONTOLOGY
    ontocount       Count ontology term(s)
    ontoget         Get ontology term(s)
    ontogetcommon   Get common ancestor for terms
    ontogetdown     Get ontology term(s) by parent id
    ontogetobsolete Get ontology ontology terms
    ontogetroot     Get ontology root terms by child identifier
    ontogetsibs     Get ontology term(s) by id with common parent
    ontogetup       Get ontology term(s) by id of child
    ontoisobsolete  Report whether an ontology term id is obsolete
    ontotext        Get ontology term(s) original full text

    ONTOLOGY EDAM
    drfinddata     Find public databases by data type
    drfindformat   Find public databases by format
    drfindid       Find public databases by identifier
    drfindresource Find public databases by resource
    edamdef        Find EDAM ontology terms by definition
    edamhasinput   Find EDAM ontology terms by has_input relation
    edamhasoutput  Find EDAM ontology terms by has_output relation
    edamisformat   Find EDAM ontology terms by is_format_of relation
    edamisid       Find EDAM ontology terms by is_identifier_of relation
    edamname       Find EDAM ontology terms by name
    wossdata       Find programs by EDAM data
    wossinput      Find programs by EDAM input data
    wossoperation  Find programs by EDAM operation
    wossoutput     Find programs by EDAM output data
    wossparam      Find programs by EDAM parameter
    wosstopic      Find programs by EDAM topic

    ONTOLOGY GO
    godef  Find GO ontology terms by definition
    goname Find GO ontology terms by name

    ONTOLOGY TAXONOMY
    taxget        Get taxon(s)
    taxgetdown    Get descendants of taxon(s)
    taxgetrank    Get parents of taxon(s)
    taxgetspecies Get all species under taxon(s)
    taxgetup      Get parents of taxon(s)

    PHYLOGENY CONSENSUS
    econsense     Majority-rule and strict consensus tree
    fconsense     Majority-rule and strict consensus tree
    ftreedist     Calculate distances between trees
    ftreedistpair Calculate distance between two sets of trees

    PHYLOGENY CONTINUOUS CHARACTERS
    econtml   Continuous character maximum likelihood method
    econtrast Continuous character contrasts
    fcontrast Continuous character contrasts

    PHYLOGENY DISCRETE CHARACTERS
    eclique   Largest clique program
    edollop   Dollo and polymorphism parsimony algorithm
    edolpenny Penny algorithm Dollo or polymorphism
    efactor   Multistate to binary recoding program
    emix      Mixed parsimony algorithm
    epenny    Penny algorithm, branch-and-bound
    fclique   Largest clique program
    fdollop   Dollo and polymorphism parsimony algorithm
    fdolpenny Penny algorithm Dollo or polymorphism
    ffactor   Multistate to binary recoding program
    fmix      Mixed parsimony algorithm
    fmove     Interactive mixed method parsimony
    fpars     Discrete character parsimony
    fpenny    Penny algorithm, branch-and-bound

    PHYLOGENY DISTANCE MATRIX
    efitch    Fitch-Margoliash and least-squares distance methods
    ekitsch   Fitch-Margoliash method with contemporary tips
    eneighbor Phylogenies from distance matrix by N-J or UPGMA method
    ffitch    Fitch-Margoliash and least-squares distance methods
    fkitsch   Fitch-Margoliash method with contemporary tips
    fneighbor Phylogenies from distance matrix by N-J or UPGMA method

    PHYLOGENY GENE FREQUENCIES
    egendist Genetic distance matrix program
    fcontml  Gene frequency and continuous character maximum likelihood
    fgendist Compute genetic distances from gene frequencies

    PHYLOGENY MOLECULAR SEQUENCE
    distmat     Create a distance matrix from a multiple sequence alignment
    ednacomp    DNA compatibility algorithm
    ednadist    Nucleic acid sequence distance matrix program
    ednainvar   Nucleic acid sequence invariants method
    ednaml      Phylogenies from nucleic acid maximum likelihood
    ednamlk     Phylogenies from nucleic acid maximum likelihood with clock
    ednapars    DNA parsimony algorithm
    ednapenny   Penny algorithm for DNA
    eprotdist   Protein distance algorithm
    eprotpars   Protein parsimony algorithm
    erestml     Restriction site maximum likelihood method
    eseqboot    Bootstrapped sequences algorithm
    fdiscboot   Bootstrapped discrete sites algorithm
    fdnacomp    DNA compatibility algorithm
    fdnadist    Nucleic acid sequence distance matrix program
    fdnainvar   Nucleic acid sequence invariants method
    fdnaml      Estimate nucleotide phylogeny by maximum likelihood
    fdnamlk     Estimates nucleotide phylogeny by maximum likelihood
    fdnamove    Interactive DNA parsimony
    fdnapars    DNA parsimony algorithm
    fdnapenny   Penny algorithm for DNA
    fdolmove    Interactive Dollo or polymorphism parsimony
    ffreqboot   Bootstrapped genetic frequencies algorithm
    fproml      Protein phylogeny by maximum likelihood
    fpromlk     Protein phylogeny by maximum likelihood
    fprotdist   Protein distance algorithm
    fprotpars   Protein parsimony algorithm
    frestboot   Bootstrapped restriction sites algorithm
    frestdist   Calculate 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        Predict protein secondary structure using GOR method
    helixturnhelix Identify nucleic acid-binding motifs in protein sequences
    pepcoil        Predict coiled coil regions in protein sequences
    pepnet         Draw a helical net for a protein sequence
    pepwheel       Draw a helical wheel diagram for a protein sequence

    PROTEIN 3D STRUCTURE
    contacts   Generate intra-chain CON files from CCF files
    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
    psiphi     Calculates phi and psi torsion angles from protein coordinates

    PROTEIN COMPOSITION
    backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
    backtranseq   Back-translate a protein sequence to a nucleotide sequence
    compseq       Calculate the composition of unique words in sequences
    emowse        Search protein sequences by digest fragment molecular weight
    freak         Generate residue/base frequency table or plot
    mwcontam      Find weights common to multiple molecular weights files
    mwfilter      Filter noisy data from molecular weights file
    oddcomp       Identify proteins with specified sequence word composition
    pepdigest     Report on protein proteolytic enzyme or reagent cleavage sites
    pepinfo       Plot amino acid properties of a protein sequence in parallel
    pepstats      Calculate statistics of protein properties
    wordcount     Count and extract unique words in molecular sequence(s)

    PROTEIN DOMAINS
    cathparse      Generate DCF file from raw CATH files
    domainalign    Generate alignments (DAF file) for nodes in a DCF file
    domainnr       Remove redundant domains from a DCF file
    domainrep      Reorder DCF file to identify representative structures
    domainseqs     Add sequence records to a DCF file
    domainsse      Add secondary structure records to a DCF file
    helixturnhelix Identify nucleic acid-binding motifs in protein sequences
    libgen         Generate discriminating elements from alignments
    matgen3d       Generate a 3D-1D scoring matrix from CCF files
    pepcoil        Predict coiled coil regions in protein sequences
    rocon          Generate a hits file from comparing two DHF files
    rocplot        Perform ROC analysis on hits files
    scopparse      Generate DCF file from raw SCOP files
    seqalign       Extend alignments (DAF file) with sequences (DHF file)
    seqfraggle     Remove fragment sequences from DHF files
    seqsort        Remove ambiguous classified sequences from DHF files
    seqwords       Generate DHF files from keyword search of UniProt
    ssematch       Search a DCF file for secondary structure matches

    PROTEIN FUNCTIONAL SITES
    echlorop  Report presence of chloroplast transit peptides
    elipop    Predict lipoproteins
    esignalp  Report protein signal cleavage sites
    etmhmm    Reports transmembrane helices
    sigcleave Report on signal cleavage sites in a protein sequence
    siggenlig Generate ligand-binding signatures from a CON file
    sigscan   Generate hits (DHF file) from a signature search
    tmap      Predict and plot transmembrane segments in protein sequences
    topo      Draw an image of a transmembrane protein

    PROTEIN MODIFICATIONS
    enetnglyc Report N-glycosylation sites in human proteins
    enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
    enetphos  Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
    eprop     Report propeptide cleavage sites in proteins
    esignalp  Report protein signal cleavage sites
    eyinoyang Report O-(beta)-GlcNAc attachment sites

    PROTEIN MOTIFS
    antigenic    Find antigenic sites in proteins
    eiprscan     Motif detection
    elipop       Predict lipoproteins
    emast        Motif detection
    ememe        Multiple EM for motif elicitation
    ememetext    Multiple EM for motif elicitation, text file only
    epestfind    Find PEST motifs as potential proteolytic cleavage sites
    fuzzpro      Search for patterns in protein sequences
    fuzztran     Search for patterns in protein sequences (translated)
    omeme        Motif detection
    patmatdb     Search protein sequences with a sequence motif
    patmatmotifs Scan a protein sequence with motifs from the PROSITE database
    preg         Regular expression search of protein sequence(s)
    pscan        Scan protein sequence(s) with fingerprints from the PRINTS database
    sigcleave    Report on signal cleavage sites in a protein sequence

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

    PROTEIN PROFILES
    profit     Scan one or more sequences with a simple frequency matrix
    prophecy   Create frequency matrix or profile from a multiple alignment
    prophet    Scan one or more sequences with a Gribskov or Henikoff profile
    seqsearch  Generate PSI-BLAST hits (DHF file) from a DAF file
    siggen     Generate 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 and writes hits (LHF file)

    PROTEIN PROPERTIES
    charge       Draw a protein charge plot
    hmoment      Calculate and plot hydrophobic moment for protein sequence(s)
    iep          Calculate the isoelectric point of proteins
    octanol      Draw a White-Wimley protein hydropathy plot
    pepinfo      Plot amino acid properties of a protein sequence in parallel
    pepstats     Calculate statistics of protein properties
    pepwindow    Draw a hydropathy plot for a protein sequence
    pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment

    TEST
    crystalball Answer every drug discovery question about a sequence

    UTILS
    embossdata    Find and retrieve EMBOSS data files
    embossupdate  Checks for more recent updates to EMBOSS
    embossversion Report the current EMBOSS version number

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

    UTILS DATABASE INDEXING
    dbiblast      Index a BLAST database
    dbifasta      Index a fasta file database
    dbiflat       Index a flat file database
    dbigcg        Index a GCG formatted database
    dbxcompress   Compress an uncompressed dbx index
    dbxedam       Index the EDAM ontology using b+tree indices
    dbxfasta      Index a fasta file database using b+tree indices
    dbxflat       Index a flat file database using b+tree indices
    dbxgcg        Index a GCG formatted database using b+tree indices
    dbxobo        Index an obo ontology using b+tree indices
    dbxreport     Validate index and report internals for dbx databases
    dbxresource   Index a data resource catalogue using b+tree indices
    dbxstat       Dump statistics for dbx databases
    dbxtax        Index NCBI taxonomy using b+tree indices
    dbxuncompress Uncompress a compressed dbx index

       Example 3

       Display an alphabetic listing of all programs:

    % wossname -search "" -alphabetic
    Find programs by keywords in their short description

    ALPHABETIC LIST OF PROGRAMS
    aaindexextract   Extract amino acid property data from AAINDEX
    abiview          Display the trace in an ABI sequencer file
    acdc             Test an application ACD file
    acdpretty        Correctly reformat an application ACD file
    acdtable         Generate an HTML table of parameters from an application ACD fi
    le
    acdtrace         Trace processing of an application ACD file (for testing)
    acdvalid         Validate an application ACD file
    aligncopy        Read and write alignments
    aligncopypair    Read and write pairs from alignments
    allversusall     Sequence similarity data from all-versus-all comparison
    antigenic        Find antigenic sites in proteins
    assemblyget      Get assembly of sequence reads
    backtranambig    Back-translate a protein sequence to ambiguous nucleotide seque
    nce
    backtranseq      Back-translate a protein sequence to a nucleotide sequence
    banana           Plot bending and curvature data for B-DNA
    biosed           Replace or delete sequence sections
    btwisted         Calculate the twisting in a B-DNA sequence
    cachedas         Generate server cache file for DAS servers or for the DAS regis
    try
    cachedbfetch     Generate server cache file for Dbfetch/WSDbfetch data sources
    cacheebeyesearch Generate server cache file for EB-eye search domains
    cacheensembl     Generate server cache file for an Ensembl server
    cai              Calculate codon adaptation index
    cathparse        Generate DCF file from raw CATH files
    chaos            Draw a chaos game representation plot for a nucleotide sequence
    charge           Draw a protein charge plot
    checktrans       Report STOP codons and ORF statistics of a protein
    chips            Calculate Nc codon usage statistic
    cirdna           Draw circular map of DNA constructs
    codcmp           Codon usage table comparison
    codcopy          Copy and reformat a codon usage table
    coderet          Extract CDS, mRNA and translations from feature tables
    compseq          Calculate the composition of unique words in sequences
    cons             Create a consensus sequence from a multiple alignment
    consambig        Create an ambiguous consensus sequence from a multiple alignmen
    t
    contacts         Generate intra-chain CON files from CCF files
    cpgplot          Identify and plot CpG islands in nucleotide sequence(s)
    cpgreport        Identify and report CpG-rich regions in nucleotide sequence(s)
    crystalball      Answer every drug discovery question about a sequence
    cusp             Create a codon usage table from nucleotide sequence(s)
    cutgextract      Extract codon usage tables from CUTG database
    cutseq           Remove a section from a sequence
    dan              Calculate nucleic acid melting temperature
    dbiblast         Index a BLAST database
    dbifasta         Index a fasta file database
    dbiflat          Index a flat file database
    dbigcg           Index a GCG formatted database
    dbtell           Display information about a public database
    dbxcompress      Compress an uncompressed dbx index
    dbxedam          Index the EDAM ontology using b+tree indices
    dbxfasta         Index a fasta file database using b+tree indices
    dbxflat          Index a flat file database using b+tree indices
    dbxgcg           Index a GCG formatted database using b+tree indices
    dbxobo           Index an obo ontology using b+tree indices
    dbxreport        Validate index and report internals for dbx databases
    dbxresource      Index a data resource catalogue using b+tree indices
    dbxstat          Dump statistics for dbx databases
    dbxtax           Index NCBI taxonomy using b+tree indices
    dbxuncompress    Uncompress a compressed dbx index
    degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
    density          Draw a nucleic acid density plot
    descseq          Alter the name or description of a sequence
    diffseq          Compare and report features of two similar sequences
    distmat          Create a distance matrix from a multiple sequence alignment
    domainalign      Generate alignments (DAF file) for nodes in a DCF file
    domainer         Generate domain CCF files from protein CCF files
    domainnr         Remove redundant domains from a DCF file
    domainrep        Reorder DCF file to identify representative structures
    domainreso       Remove low resolution domains from a DCF file
    domainseqs       Add sequence records to a DCF file
    domainsse        Add secondary structure records to a DCF file
    dotmatcher       Draw a threshold dotplot of two sequences
    dotpath          Draw a non-overlapping wordmatch dotplot of two sequences
    dottup           Display a wordmatch dotplot of two sequences
    dreg             Regular expression search of nucleotide sequence(s)
    drfinddata       Find public databases by data type
    drfindformat     Find public databases by format
    drfindid         Find public databases by identifier
    drfindresource   Find public databases by resource
    drget            Get data resource entries
    drtext           Get data resource entries complete text
    echlorop         Report presence of chloroplast transit peptides
    eclique          Largest clique program
    econsense        Majority-rule and strict consensus tree
    econtml          Continuous character maximum likelihood method
    econtrast        Continuous character contrasts
    edamdef          Find EDAM ontology terms by definition
    edamhasinput     Find EDAM ontology terms by has_input relation
    edamhasoutput    Find EDAM ontology terms by has_output relation
    edamisformat     Find EDAM ontology terms by is_format_of relation
    edamisid         Find EDAM ontology terms by is_identifier_of relation
    edamname         Find EDAM ontology terms by name
    edialign         Local multiple alignment of sequences
    ednacomp         DNA compatibility algorithm
    ednadist         Nucleic acid sequence distance matrix program
    ednainvar        Nucleic acid sequence invariants method
    ednaml           Phylogenies from nucleic acid maximum likelihood
    ednamlk          Phylogenies from nucleic acid maximum likelihood with clock
    ednapars         DNA parsimony algorithm
    ednapenny        Penny algorithm for DNA
    edollop          Dollo and polymorphism parsimony algorithm
    edolpenny        Penny algorithm Dollo or polymorphism
    efactor          Multistate to binary recoding program
    efitch           Fitch-Margoliash and least-squares distance methods
    egendist         Genetic distance matrix program
    ehmmalign        Align sequences to an HMM profile
    ehmmbuild        Build a profile HMM from an alignment
    ehmmcalibrate    Calibrate HMM search statistics
    ehmmconvert      Convert between profile HMM file formats
    ehmmemit         Generate sequences from a profile HMM
    ehmmfetch        Retrieve an HMM from an HMM database
    ehmmindex        Create a binary SSI index for an HMM database
    ehmmpfam         Search one or more sequences against an HMM database
    ehmmsearch       Search a sequence database with a profile HMM
    einverted        Find inverted repeats in nucleotide sequences
    eiprscan         Motif detection
    ekitsch          Fitch-Margoliash method with contemporary tips
    elipop           Predict lipoproteins
    emast            Motif detection
    embossdata       Find and retrieve EMBOSS data files
    embossupdate     Checks for more recent updates to EMBOSS
    embossversion    Report the current EMBOSS version number
    ememe            Multiple EM for motif elicitation
    ememetext        Multiple EM for motif elicitation, text file only
    emira            MIRA fragment assembly program
    emiraest         MIRAest fragment assembly program
    emix             Mixed parsimony algorithm
    emma             Multiple sequence alignment (ClustalW wrapper)
    emnu             Simple menu of EMBOSS applications
    emowse           Search protein sequences by digest fragment molecular weight
    eneighbor        Phylogenies from distance matrix by N-J or UPGMA method
    enetnglyc        Report N-glycosylation sites in human proteins
    enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian pr
    oteins
    enetphos         Report Ser, Thr and Tyr phosphorylation sites in eukaryotic pro
    teins
    entret           Retrieve sequence entries from flatfile databases and files
    eomega           Multiple sequence alignment (ClustalO wrapper)
    eomegapp         Profile with profile (ClustalO wrapper)
    eomegash         Sequence with HMM (ClustalO wrapper)
    eomegasp         Sequence with profile (ClustalO wrapper)
    epenny           Penny algorithm, branch-and-bound
    epestfind        Find PEST motifs as potential proteolytic cleavage sites
    eprimer3         Pick PCR primers and hybridization oligos
    eprimer32        Pick PCR primers and hybridization oligos
    eprop            Report propeptide cleavage sites in proteins
    eprotdist        Protein distance algorithm
    eprotpars        Protein parsimony algorithm
    equicktandem     Find tandem repeats in nucleotide sequences
    erestml          Restriction site maximum likelihood method
    eseqboot         Bootstrapped sequences algorithm
    esignalp         Report protein signal cleavage sites
    esim4            Align an mRNA to a genomic DNA sequence
    est2genome       Align EST sequences to genomic DNA sequence
    etandem          Find tandem repeats in a nucleotide sequence
    etmhmm           Reports transmembrane helices
    extractalign     Extract regions from a sequence alignment
    extractfeat      Extract features from sequence(s)
    extractseq       Extract regions from a sequence
    eyinoyang        Report O-(beta)-GlcNAc attachment sites
    fclique          Largest clique program
    fconsense        Majority-rule and strict consensus tree
    fcontml          Gene frequency and continuous character maximum likelihood
    fcontrast        Continuous character contrasts
    fdiscboot        Bootstrapped discrete sites algorithm
    fdnacomp         DNA compatibility algorithm
    fdnadist         Nucleic acid sequence distance matrix program
    fdnainvar        Nucleic acid sequence invariants method
    fdnaml           Estimate nucleotide phylogeny by maximum likelihood
    fdnamlk          Estimates nucleotide phylogeny by maximum likelihood
    fdnamove         Interactive DNA parsimony
    fdnapars         DNA parsimony algorithm
    fdnapenny        Penny algorithm for DNA
    fdollop          Dollo and polymorphism parsimony algorithm
    fdolmove         Interactive Dollo or polymorphism parsimony
    fdolpenny        Penny algorithm Dollo or polymorphism
    fdrawgram        Plots a cladogram- or phenogram-like rooted tree diagram
    fdrawtree        Plots an unrooted tree diagram
    featcopy         Read and write a feature table
    featmerge        Merge two overlapping feature tables
    featreport       Read and write a feature table
    feattext         Return a feature table original text
    ffactor          Multistate to binary recoding program
    ffitch           Fitch-Margoliash and least-squares distance methods
    ffreqboot        Bootstrapped genetic frequencies algorithm
    fgendist         Compute genetic distances from gene frequencies
    findkm           Calculate and plot enzyme reaction data
    fkitsch          Fitch-Margoliash method with contemporary tips
    fmix             Mixed parsimony algorithm
    fmove            Interactive mixed method parsimony
    fneighbor        Phylogenies from distance matrix by N-J or UPGMA method
    fpars            Discrete character parsimony
    fpenny           Penny algorithm, branch-and-bound
    fproml           Protein phylogeny by maximum likelihood
    fpromlk          Protein phylogeny by maximum likelihood
    fprotdist        Protein distance algorithm
    fprotpars        Protein parsimony algorithm
    freak            Generate residue/base frequency table or plot
    frestboot        Bootstrapped restriction sites algorithm
    frestdist        Calculate 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        Calculate distances between trees
    ftreedistpair    Calculate distance between two sets of trees
    fuzznuc          Search for patterns in nucleotide sequences
    fuzzpro          Search for patterns in protein sequences
    fuzztran         Search for patterns in protein sequences (translated)
    garnier          Predict protein secondary structure using GOR method
    geecee           Calculate fractional GC content of nucleic acid sequences
    getorf           Find and extract open reading frames (ORFs)
    godef            Find GO ontology terms by definition
    goname           Find GO ontology terms by name
    helixturnhelix   Identify nucleic acid-binding motifs in protein sequences
    hetparse         Convert heterogen group dictionary to EMBL-like format
    hmoment          Calculate and plot hydrophobic moment for protein sequence(s)
    iep              Calculate the isoelectric point of proteins
    infoalign        Display basic information about a multiple sequence alignment
    infoassembly     Display information about assemblies
    infobase         Return information on a given nucleotide base
    inforesidue      Return information on a given amino acid residue
    infoseq          Display basic information about sequences
    interface        Generate inter-chain CON files from CCF files
    isochore         Plot isochores in DNA sequences
    jaspextract      Extract data from JASPAR
    jaspscan         Scan DNA sequences for transcription factors
    libgen           Generate discriminating elements from alignments
    lindna           Draw linear maps of DNA constructs
    listor           Write a list file of the logical OR of two sets of sequences
    makenucseq       Create random nucleotide sequences
    makeprotseq      Create random protein sequences
    marscan          Find matrix/scaffold recognition (MRS) signatures in DNA sequen
    ces
    maskambignuc     Mask all ambiguity characters in nucleotide sequences with N
    maskambigprot    Mask all ambiguity characters in protein sequences with X
    maskfeat         Write a sequence with masked features
    maskseq          Write a sequence with masked regions
    matcher          Waterman-Eggert local alignment of two sequences
    matgen3d         Generate a 3D-1D scoring matrix from CCF files
    megamerger       Merge two large overlapping DNA sequences
    merger           Merge two overlapping sequences
    msbar            Mutate a sequence
    mse              Multiple sequence editor
    mwcontam         Find weights common to multiple molecular weights files
    mwfilter         Filter noisy data from molecular weights file
    needle           Needleman-Wunsch global alignment of two sequences
    needleall        Many-to-many pairwise alignments of two sequence sets
    newcpgreport     Identify CpG islands in nucleotide sequence(s)
    newcpgseek       Identify and report CpG-rich regions in nucleotide sequence(s)
    newseq           Create a sequence file from a typed-in sequence
    nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
    noreturn         Remove carriage return from ASCII files
    nospace          Remove whitespace from an ASCII text file
    notab            Replace tabs with spaces in an ASCII text file
    notseq           Write to file a subset of an input stream of sequences
    nthseq           Write to file a single sequence from an input stream of sequenc
    es
    nthseqset        Read and write (return) one set of sequences from many
    oalistat         Statistics for multiple alignment files
    octanol          Draw a White-Wimley protein hydropathy plot
    oddcomp          Identify proteins with specified sequence word composition
    ohmmalign        Align sequences with an HMM
    ohmmbuild        Build HMM
    ohmmcalibrate    Calibrate a hidden Markov model
    ohmmconvert      Convert between HMM formats
    ohmmemit         Extract HMM sequences
    ohmmfetch        Extract HMM from a database
    ohmmindex        Index an HMM database
    ohmmpfam         Align single sequence with an HMM
    ohmmsearch       Search sequence database with an HMM
    omeme            Motif detection
    ontocount        Count ontology term(s)
    ontoget          Get ontology term(s)
    ontogetcommon    Get common ancestor for terms
    ontogetdown      Get ontology term(s) by parent id
    ontogetobsolete  Get ontology ontology terms
    ontogetroot      Get ontology root terms by child identifier
    ontogetsibs      Get ontology term(s) by id with common parent
    ontogetup        Get ontology term(s) by id of child
    ontoisobsolete   Report whether an ontology term id is obsolete
    ontotext         Get ontology term(s) original full text
    ovrnaalifold     Calculate secondary structures for a set of aligned RNAs
    ovrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs (parti
    tion)
    ovrnacofold      Calculate secondary structures of RNA dimers
    ovrnacofoldconc  Calculate secondary structures of RNA dimers (concentrations)
    ovrnacofoldpf    Calculate secondary structures of RNA dimers (partitioning)
    ovrnadistance    Calculate distances between RNA secondary structures
    ovrnaduplex      Predict RNA duplex (hybridization) sites and structure
    ovrnaeval        Calculate energy of RNA sequences with a given secondary struct
    ure
    ovrnaevalpair    Calculate energy of RNA sequences on given secondary structure
    ovrnafold        Calculate min. energy RNA structure / pair probabilities (parti
    tion)
    ovrnafoldpf      Calculate min. energy RNA structure / pair probabilities
    ovrnaheat        Calculate specific heat of RNA melting
    ovrnainverse     Find RNA sequences with a given secondary structure
    ovrnalfold       Calculate locally stable secondary structures of RNAs
    ovrnaplot        Draw RNA secondary structures
    ovrnasubopt      Calculate suboptimal secondary structure of RNA
    palindrome       Find inverted repeats in nucleotide sequence(s)
    pasteseq         Insert one sequence into another
    patmatdb         Search protein sequences with a sequence motif
    patmatmotifs     Scan a protein sequence with motifs from the PROSITE database
    pdbparse         Parse PDB files and writes protein CCF files
    pdbplus          Add accessibility and secondary structure to a CCF file
    pdbtosp          Convert swissprot:PDB codes file to EMBL-like format
    pepcoil          Predict coiled coil regions in protein sequences
    pepdigest        Report on protein proteolytic enzyme or reagent cleavage sites
    pepinfo          Plot amino acid properties of a protein sequence in parallel
    pepnet           Draw a helical net for a protein sequence
    pepstats         Calculate statistics of protein properties
    pepwheel         Draw a helical wheel diagram for a protein sequence
    pepwindow        Draw a hydropathy plot for a protein sequence
    pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein alignment
    plotcon          Plot conservation of a sequence alignment
    plotorf          Plot potential open reading frames in a nucleotide sequence
    polydot          Draw dotplots for all-against-all comparison of a sequence set
    preg             Regular expression search of protein sequence(s)
    prettyplot       Draw a sequence alignment with pretty formatting
    prettyseq        Write a nucleotide sequence and its translation to file
    primersearch     Search DNA sequences for matches with primer pairs
    printsextract    Extract data from PRINTS database for use by pscan
    profit           Scan one or more sequences with a simple frequency matrix
    prophecy         Create frequency matrix or profile from a multiple alignment
    prophet          Scan one or more sequences with a Gribskov or Henikoff profile
    prosextract      Process the PROSITE motif database for use by patmatmotifs
    pscan            Scan protein sequence(s) with fingerprints from the PRINTS data
    base
    psiphi           Calculates phi and psi torsion angles from protein coordinates
    rebaseextract    Process the REBASE database for use by restriction enzyme appli
    cations
    recoder          Find restriction sites to remove (mutate) with no translation c
    hange
    redata           Retrieve information from REBASE restriction enzyme database
    refseqget        Get reference sequence
    remap            Display restriction enzyme binding sites in a nucleotide sequen
    ce
    restover         Find restriction enzymes producing a specific overhang
    restrict         Report restriction enzyme cleavage sites in a nucleotide sequen
    ce
    revseq           Reverse and complement a nucleotide sequence
    rocon            Generate a hits file from comparing two DHF files
    rocplot          Perform ROC analysis on hits files
    scopparse        Generate DCF file from raw SCOP files
    seealso          Find programs with similar function to a specified program
    seqalign         Extend alignments (DAF file) with sequences (DHF file)
    seqcount         Read and count sequences
    seqfraggle       Remove fragment sequences from DHF files
    seqmatchall      All-against-all word comparison of a sequence set
    seqnr            Remove redundancy from DHF files
    seqret           Read and write (return) sequences
    seqretsetall     Read and write (return) many sets of sequences
    seqretsplit      Read sequences and write them to individual files
    seqsearch        Generate PSI-BLAST hits (DHF file) from a DAF file
    seqsort          Remove ambiguous classified sequences from DHF files
    seqwords         Generate DHF files from keyword search of UniProt
    seqxref          Retrieve all database cross-references for a sequence entry
    seqxrefget       Retrieve all cross-referenced data for a sequence entry
    servertell       Display information about a public server
    showalign        Display a multiple sequence alignment in pretty format
    showdb           Display information on configured databases
    showfeat         Display features of a sequence in pretty format
    showorf          Display a nucleotide sequence and translation in pretty format
    showpep          Display protein sequences with features in pretty format
    showseq          Display sequences with features in pretty format
    showserver       Display information on configured servers
    shuffleseq       Shuffle a set of sequences maintaining composition
    sigcleave        Report on signal cleavage sites in a protein sequence
    siggen           Generate 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 and writes hits (LHF file)
    silent           Find restriction sites to insert (mutate) with no translation c
    hange
    sirna            Find siRNA duplexes in mRNA
    sites            Generate residue-ligand CON files from CCF files
    sixpack          Display a DNA sequence with 6-frame translation and ORFs
    sizeseq          Sort sequences by size
    skipredundant    Remove redundant sequences from an input set
    skipseq          Read and write (return) sequences, skipping first few
    splitsource      Split sequence(s) into original source sequences
    splitter         Split sequence(s) into smaller sequences
    ssematch         Search a DCF file for secondary structure matches
    stretcher        Needleman-Wunsch rapid global alignment of two sequences
    stssearch        Search a DNA database for matches with a set of STS primers
    supermatcher     Calculate approximate local pair-wise alignments of larger sequ
    ences
    syco             Draw synonymous codon usage statistic plot for a nucleotide seq
    uence
    taxget           Get taxon(s)
    taxgetdown       Get descendants of taxon(s)
    taxgetrank       Get parents of taxon(s)
    taxgetspecies    Get all species under taxon(s)
    taxgetup         Get parents of taxon(s)
    tcode            Identify protein-coding regions using Fickett TESTCODE statisti
    c
    textget          Get text data entries
    textsearch       Search the textual description of sequence(s)
    tfextract        Process TRANSFAC transcription factor database for use by tfsca
    n
    tfm              Display full documentation for an application
    tfscan           Identify transcription factor binding sites in DNA sequences
    tmap             Predict and plot transmembrane segments in protein sequences
    topo             Draw an image of a transmembrane protein
    tranalign        Generate an alignment of nucleic coding regions from aligned pr
    oteins
    transeq          Translate nucleic acid sequences
    trimest          Remove poly-A tails from nucleotide sequences
    trimseq          Remove unwanted characters from start and end of sequence(s)
    trimspace        Remove extra whitespace from an ASCII text file
    twofeat          Find neighbouring pairs of features in sequence(s)
    union            Concatenate multiple sequences into a single sequence
    urlget           Get URLs of data resources
    variationget     Get sequence variations
    vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
    vrna2dfold       Calculate RNA structures and samples of k,l neighbourhoods
    vrnaaliduplex    RNA duplex calculation for two sequence alignments
    vrnaalifold      Calculate secondary structures for a set of aligned RNAs
    vrnaalifoldpf    Calculate secondary structures for a set of aligned RNAs (parti
    tion)
    vrnacofold       Calculate secondary structures of RNA dimers
    vrnacofoldconc   Calculate secondary structures of RNA dimers (concentrations)
    vrnacofoldpf     Calculate secondary structures of RNA dimers (partitioning)
    vrnadistance     Calculate distances between RNA secondary structures
    vrnaduplex       Predict RNA duplex (hybridization) sites and structure
    vrnaeval         Calculate energy of RNA sequences with a given secondary struct
    ure
    vrnaevalpair     Calculate energy of RNA sequences on given secondary structure
    vrnafold         Calculate min. energy RNA secondary structures and pair probabi
    lities
    vrnafoldpf       Calculate min. energy RNA structures / pair probabilities (part
    ition)
    vrnaheat         Calculate specific heat of RNA melting
    vrnainverse      Find RNA sequences with a given secondary structure
    vrnalalifoldpf   Calculate secondary structures for a set of aligned RNAs (parti
    tion)
    vrnalfold        Calculate locally stable secondary structures of RNAs
    vrnalfoldz       Calculate locally stable secondary structures of RNAs plus zsco
    re
    vrnapkplex       Calculate RNA structures plus pseudoknots
    vrnaplfold       Compute avg. pair probabilities for local base pairs in RNA seq
    uences
    vrnaplot         Draw RNA secondary structures
    vrnasubopt       Calculate suboptimal secondary structures of RNAs
    water            Smith-Waterman local alignment of sequences
    whichdb          Search all sequence databases for an entry and retrieve it
    wobble           Plot third base position variability in a nucleotide sequence
    wordcount        Count and extract unique words in molecular sequence(s)
    wordfinder       Match large sequences against one or more other sequences
    wordmatch        Find regions of identity (exact matches) of two sequences
    wossdata         Find programs by EDAM data
    wossinput        Find programs by EDAM input data
    wossname         Find programs by keywords in their short description
    wossoperation    Find programs by EDAM operation
    wossoutput       Find programs by EDAM output data
    wossparam        Find programs by EDAM parameter
    wosstopic        Find programs by EDAM topic
    yank             Add a sequence reference (a full USA) to a list file

       Example 4

       Display only the groups that the programs can belong to:

    % wossname -search "" -groups
    Find programs by keywords in their short description

    ACD
    ALIGNMENT
    ALIGNMENT CONSENSUS
    ALIGNMENT DIFFERENCES
    ALIGNMENT DOT PLOTS
    ALIGNMENT GLOBAL
    ALIGNMENT LOCAL
    ALIGNMENT MULTIPLE
    ASSEMBLY FRAGMENT ASSEMBLY
    DATA RESOURCES
    DATA RETRIEVAL
    DATA RETRIEVAL CHEMISTRY DATA
    DATA RETRIEVAL FEATURE DATA
    DATA RETRIEVAL ONTOLOGY DATA
    DATA RETRIEVAL RESOURCE DATA
    DATA RETRIEVAL SEQUENCE DATA
    DATA RETRIEVAL SEQUENCE DATA ASSEMBLY DATA
    DATA RETRIEVAL TEXT DATA
    DATA RETRIEVAL TOOL DATA
    DATA RETRIEVAL URL DATA
    DISPLAY
    DOCUMENTATION
    EDIT
    ENZYME KINETICS
    FEATURE TABLES
    HMM
    MENUS
    NUCLEIC 2D STRUCTURE
    NUCLEIC CODON USAGE
    NUCLEIC COMPOSITION
    NUCLEIC CPG ISLANDS
    NUCLEIC FUNCTIONAL SITES
    NUCLEIC GENE FINDING
    NUCLEIC MOTIFS
    NUCLEIC MUTATION
    NUCLEIC PRIMERS
    NUCLEIC PROFILES
    NUCLEIC PROPERTIES
    NUCLEIC REPEATS
    NUCLEIC RESTRICTION
    NUCLEIC RNA FOLDING
    NUCLEIC TRANSCRIPTION
    NUCLEIC TRANSLATION
    ONTOLOGY
    ONTOLOGY EDAM
    ONTOLOGY GO
    ONTOLOGY TAXONOMY
    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 DOMAINS
    PROTEIN FUNCTIONAL SITES
    PROTEIN MODIFICATIONS
    PROTEIN MOTIFS
    PROTEIN MUTATION
    PROTEIN PROFILES
    PROTEIN PROPERTIES
    TEST
    UTILS
    UTILS DATABASE CREATION
    UTILS DATABASE INDEXING

       Example 5

       Output html tags around the list of programs:

    % wossname "" -html -out wossname.html
    Find programs by keywords in their short description

       Go to the output files for this example

    Command line arguments

    Find programs by keywords in their short description
    Version: EMBOSS:6.5.6.0

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

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

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

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

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

    Input file format

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

       The format of ACD files is documented elsewhere.

    Output file format

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

      Output files for usage example 5

      File: wossname.html

       ACD  Program name Description
        acdc Test an application ACD
       file   acdpretty
       Correctly reformat an application ACD file   acdtable Generate an HTML table of
       parameters from an application ACD file   acdtrace Trace processing of an
       application ACD file (for testing)   acdvalid Validate an application ACD
       file   ALIGNMENT
        Program
       name Description  extractalign Extract regions from
       a sequence alignment   ALIGNMENT CONSENSUS  Program name Description
        cons Create a consensus
       sequence from a multiple alignment   [Part of this file
       has been deleted for brevity]  dbxedam Index the EDAM ontology using
       b+tree indices   dbxfasta Index a fasta file database
       using b+tree indices   dbxflat Index a flat file database
       using b+tree indices   dbxgcg Index a GCG formatted database
       using b+tree indices   dbxobo Index an obo ontology using
       b+tree indices   dbxreport Validate index and report
       internals for dbx databases   dbxresource Index a data resource
       catalogue using b+tree indices   dbxstat Dump statistics for dbx
       databases   dbxtax
       Index NCBI taxonomy using b+tree indices   dbxuncompress Uncompress a
       compressed dbx index

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

    Data files

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

    Notes

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

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

    References

       None.

    Warnings

       None.

    Diagnostic Error Messages

       None.

    Exit status

       It always exits with status 0

    Known bugs

       None.

    See also

                        Program name                         Description
                        seealso       Find programs with similar function to a specified program
                        tfm           Display full documentation for an application
                        wossdata      Find programs by EDAM data
                        wossinput     Find programs by EDAM input data
       wossoperation    Find programs by EDAM operation
                        wossoutput    Find programs by EDAM output data
                        wossparam     Find programs by EDAM parameter
                        wosstopic     Find programs by EDAM topic

    Author(s)

       Gary             Williams formerly at:
       MRC              Rosalind Franklin Centre for Genomics Research Wellcome Trust
       Genome           Campus, Hinxton, Cambridge, CB10 1SB, UK

                        Please report all bugs to the EMBOSS bug team
                        (emboss-bug (c) emboss.open-bio.org) not to the original author.

    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

    Display full documentation for an application
    Version: EMBOSS:6.5.6.0

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

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

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

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

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

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

## Input file format

None.

## Output file format

Text documentation is output.

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

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

## Data files

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

## Notes

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

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

Paged text output to the screen

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

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

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

## References

None.

## Warnings

None.

## Diagnostic Error Messages

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

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
seealso | Find programs with similar function to a specified program
wossdata | Find programs by EDAM data
wossinput | Find programs by EDAM input data
wossname | Find programs by keywords in their short description
wossoperation | Find programs by EDAM operation
wossoutput | Find programs by EDAM output data
wossparam | Find programs by EDAM parameter
wosstopic | Find programs by EDAM topic

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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