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  EMBOSS
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<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
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<b><font size="+6">
tfm
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<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Display full documentation for an application

<H2>
    Description
</H2>

<p><b>tfm</b> displays help information for the specified EMBOSS program.</p>

<H2>
    Usage
</H2>
Here is a sample session with <b>tfm</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>tfm wossname </b>
Display full documentation for an application

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/homes/user/local/share/EMBOSS/doc/programs/text/wossname.txt
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                                  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)
eomegaps   Single sequence 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)
xmltext    Get XML document original full text

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

DATA RETRIEVAL XML DATA
xmlget Get XML data

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  Check 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     Check 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)
eomegaps         Single sequence 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
xmlget           Get XML data
xmltext          Get XML document original full text
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
DATA RETRIEVAL XML 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:6.6.0.0

   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

   <h2><a name="ACD">ACD</a></h2> <table border cellpadding=4
   bgcolor="#FFFFF0"> <tr><th>Program name</th> <th>Description</th></tr>
   <tr> <td><a href="acdc.html">acdc</a></td> <td>Test an application ACD
   file</td> </tr> <tr> <td><a href="acdpretty.html">acdpretty</a></td>
   <td>Correctly reformat an application ACD file</td> </tr> <tr> <td><a
   href="acdtable.html">acdtable</a></td> <td>Generate an HTML table of
   parameters from an application ACD file</td> </tr> <tr> <td><a
   href="acdtrace.html">acdtrace</a></td> <td>Trace processing of an
   application ACD file (for testing)</td> </tr> <tr> <td><a
   href="acdvalid.html">acdvalid</a></td> <td>Validate an application ACD
   file</td> </tr> </table> <h2><a name="ALIGNMENT">ALIGNMENT</a></h2>
   <table border cellpadding=4 bgcolor="#FFFFF0"> <tr><th>Program
   name</th> <th>Description</th></tr> <tr> <td><a
   href="extractalign.html">extractalign</a></td> <td>Extract regions from
   a sequence alignment</td> </tr> </table> <h2><a name="ALIGNMENT
   CONSENSUS">ALIGNMENT CONSENSUS</a></h2> <table border cellpadding=4
   bgcolor="#FFFFF0"> <tr><th>Program name</th> <th>Description</th></tr>
   <tr> <td><a href="cons.html">cons</a></td> <td>Create a consensus
   sequence from a multiple alignment</td> </tr> <tr> [Part of this file
   has been deleted for brevity] <tr> <td><a
   href="dbxedam.html">dbxedam</a></td> <td>Index the EDAM ontology using
   b+tree indices</td> </tr> <tr> <td><a
   href="dbxfasta.html">dbxfasta</a></td> <td>Index a fasta file database
   using b+tree indices</td> </tr> <tr> <td><a
   href="dbxflat.html">dbxflat</a></td> <td>Index a flat file database
   using b+tree indices</td> </tr> <tr> <td><a
   href="dbxgcg.html">dbxgcg</a></td> <td>Index a GCG formatted database
   using b+tree indices</td> </tr> <tr> <td><a
   href="dbxobo.html">dbxobo</a></td> <td>Index an obo ontology using
   b+tree indices</td> </tr> <tr> <td><a
   href="dbxreport.html">dbxreport</a></td> <td>Validate index and report
   internals for dbx databases</td> </tr> <tr> <td><a
   href="dbxresource.html">dbxresource</a></td> <td>Index a data resource
   catalogue using b+tree indices</td> </tr> <tr> <td><a
   href="dbxstat.html">dbxstat</a></td> <td>Dump statistics for dbx
   databases</td> </tr> <tr> <td><a href="dbxtax.html">dbxtax</a></td>
   <td>Index NCBI taxonomy using b+tree indices</td> </tr> <tr> <td><a
   href="dbxuncompress.html">dbxuncompress</a></td> <td>Uncompress a
   compressed dbx index</td> </tr> </table>

   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 <HTML>, <BODY>, </BODY> and </HTML> 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

</pre></td></tr></table><p>
<p>
<p>


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Display full documentation for an application
Version: EMBOSS:6.6.0.0

   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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-program]<br>(Parameter 1)</td>
<td>string</td>
<td>Enter the name of an EMBOSS program</td>
<td>Any string of at least 1 characters</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Program documentation text output file</td>
<td>Output file</td>
<td>stdout</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-html</td>
<td>boolean</td>
<td>This will format the output for displaying as a WWW document.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-more</td>
<td>boolean</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>@(!$(html))</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H2>
    Input file format
</H2>

None.

<p>


<H2>
    Output file format
</H2>

Text documentation is output.

<P>

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

<p>

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

<p>





<H2>
    Data files
</H2>

The original data for the documentation can be found in:
<A
HREF="http://emboss.sourceforge.net/apps/">http://emboss.sourceforge.net/apps/</A>
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.


<H2>
    Notes
</H2>

<p>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 <b>tfm</b> as plain text. The documentation for all current and some past releases is provided by the developers at <a href="http://emboss.sourceforge.net/apps/">http://emboss.sourceforge.net/apps/</a>. 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).</p>


<p>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!)</p>

Paged text output to the screen
<p><b>tfm</b> 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 <tt>more</tt> to display the information. This behaviour can be turned off by using the qualifier -nomore.</p>

The program <tt>more</tt> 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 <tt>less</tt> (which has more functionality than <tt>more</tt> and is used by many people). The UNIX environment variable <tt>PAGER</tt> can be set to hold the name of your preferred program. If you have PAGER set, then <b>tfm</b> will use this specified program instead of using the default <tt>more</tt> program. (If you want <b>tfm</b> to use a specified program that is different to the normal <tt>PAGER</tt> program, then <tt>PAGER</tt> can be overriden by setting the environment variable <tt>EMBOSS_PAGER</tt> to hold the name of the program that should only be used to display text in <b>tfm</b>).  <tt>PAGER</tt> can be set in UNIX with <tt>setenv PAGER less</tt>.  </p>

<p>To get help on <tt>more</tt> when using it to display text, press the <tt>?</tt> key. To get help on <tt>less</tt> when using it to display text, press the <tt>h</tt> key. </p>


<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

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


<H2>
    Exit status
</H2>

It always exits with status 0.

<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="seealso.html">seealso</a></td>
<td>Find programs with similar function to a specified program</td>
</tr>

<tr>
<td><a href="wossdata.html">wossdata</a></td>
<td>Find programs by EDAM data</td>
</tr>

<tr>
<td><a href="wossinput.html">wossinput</a></td>
<td>Find programs by EDAM input data</td>
</tr>

<tr>
<td><a href="wossname.html">wossname</a></td>
<td>Find programs by keywords in their short description</td>
</tr>

<tr>
<td><a href="wossoperation.html">wossoperation</a></td>
<td>Find programs by EDAM operation</td>
</tr>

<tr>
<td><a href="wossoutput.html">wossoutput</a></td>
<td>Find programs by EDAM output data</td>
</tr>

<tr>
<td><a href="wossparam.html">wossparam</a></td>
<td>Find programs by EDAM parameter</td>
</tr>

<tr>
<td><a href="wosstopic.html">wosstopic</a></td>
<td>Find programs by EDAM topic</td>
</tr>

</table>


<H2>
    Author(s)
</H2>
Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>

Written: 4 Aug 2000.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.


<H2>
    Comments
</H2>
None

</BODY>
</HTML>