tfm

 

Wiki

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

Please help by correcting and extending the Wiki pages.

Function

Displays full documentation for an application

Description

tfm displays help information for the specified EMBOSS program.

Usage

Here is a sample session with tfm


% tfm wossname 
Displays full documentation for an application

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

                                 wossname 



Wiki

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

Function

   Finds programs by keywords in their short description

Description

   wossname search 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 
Finds programs by keywords in their short description

SEARCH FOR 'RESTRICT'
erestml       Restriction site Maximum Likelihood method
frestboot     Bootstrapped restriction sites algorithm
frestdist     Distance matrix from restriction sites or fragments
frestml       Restriction site maximum Likelihood method
rebaseextract Process the REBASE database for use by restriction enzyme applica
tions
recoder       Find restriction sites to remove (mutate) with no translation cha
nge
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       Displays sequences with features in pretty format
silent        Find restriction sites to insert (mutate) with no translation cha
nge


   Example 2

   Display a listing of programs in their groups:


% wossname -search '' 
Finds 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 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     Displays 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
stretcher  Needleman-Wunsch rapid global alignment of two sequences

ALIGNMENT LOCAL
matcher      Waterman-Eggert local alignment of two sequences
seqmatchall  All-against-all word comparison of a sequence set
supermatcher Calculate approximate local pair-wise alignments of larger sequenc
es
water        Smith-Waterman local alignment of sequences
wordfinder   Match large sequences against one or more other sequences
wordmatch    Finds regions of identity (exact matches) of two sequences

ALIGNMENT MULTIPLE
edialign   Local multiple alignment of sequences
emma       Multiple sequence alignment (ClustalW 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 protein
s

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

DISPLAY
abiview    Display the trace in an ABI sequencer file
cirdna     Draws circular maps of DNA constructs
lindna     Draws linear maps of DNA constructs
pepnet     Draw a helical net for a protein sequence
pepwheel   Draw a helical wheel diagram for a protein 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
seealso    Finds programs with similar function to a specified program
showalign  Display a multiple sequence alignment in pretty format
showdb     Displays information on configured databases
showfeat   Display features of a sequence in pretty format
showpep    Displays protein sequences with features in pretty format
showseq    Displays sequences with features in pretty format
sixpack    Display a DNA sequence with 6-frame translation and ORFs
textsearch Search the textual description of sequence(s)

EDIT
aligncopy     Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed        Replace or delete sequence sections
codcopy       Copy and reformat a codon usage table
cutseq        Removes a section from a sequence
degapseq      Removes non-alphabetic (e.g. gap) characters from sequences
descseq       Alter the name or description of a sequence
entret        Retrieves 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      Reads and writes a feature table
featreport    Reads and writes a feature table
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  Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks 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 all 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     Reads and writes (returns) one set of sequences from many
pasteseq      Insert one sequence into another
revseq        Reverse and complement a nucleotide sequence
seqret        Reads and writes (returns) sequences
seqretsetall  Reads and writes (returns) many sets of sequences
seqretsplit   Reads sequences and writes them to individual files
sizeseq       Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq       Reads and writes (returns) 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   Removes 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
coderet     Extract CDS, mRNA and translations from 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     Finds 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
oalistat      Statistics for multiple alignment files
ohmmalign     Align sequences with an HMM
ohmmbuild     Build HMM
ohmmcalibrate Calibrate a hidden Markov model
ohmmconvert   Convert between HMM formats
ohmmemit      Extract HMM sequences
ohmmfetch     Extract HMM from a database
ohmmindex     Index an HMM database
ohmmpfam      Align single sequence with an HMM
ohmmsearch    Search sequence database with an HMM

INFORMATION
infoalign   Display basic information about a multiple sequence alignment
infobase    Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue
infoseq     Display basic information about sequences
seealso     Finds programs with similar function to a specified program
showdb      Displays information on configured databases
textsearch  Search the textual description of sequence(s)
tfm         Displays full documentation for an application
whichdb     Search all sequence databases for an entry and retrieve it
wossname    Finds programs by keywords in their short description

MENUS
emnu   Simple menu of EMBOSS applications

NUCLEIC 2D STRUCTURE
einverted      Finds inverted repeats in nucleotide sequences
vrnaalifold    RNA alignment folding
vrnaalifoldpf  RNA alignment folding with partition
vrnacofold     RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf   RNA cofolding with partitioning
vrnadistance   RNA distances
vrnaduplex     RNA duplex calculation
vrnaeval       RNA eval
vrnaevalpair   RNA eval with cofold
vrnafold       Calculate secondary structures of RNAs
vrnafoldpf     Secondary structures of RNAs with partition
vrnaheat       RNA melting
vrnainverse    RNA sequences matching a structure
vrnalfold      Calculate locally stable secondary structures of RNAs
vrnaplot       Plot vrnafold output
vrnasubopt     Calculate RNA suboptimals

NUCLEIC CODON USAGE
cai    Calculate codon adaptation index
chips  Calculates Nc codon usage statistic
codcmp Codon usage table comparison
cusp   Create a codon usage table from nucleotide sequence(s)
syco   Draw synonymous codon usage statictic 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       Calculates nucleic acid melting temperature
density   Draw a nucleic acid density plot
freak     Generate residue/base frequency table or plot
isochore  Plots isochores in DNA sequences
sirna     Finds siRNA duplexes in mRNA
wordcount Count and extract unique words in DNA 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 GENE FINDING
getorf  Finds and extracts open reading frames (ORFs)
marscan Finds 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 statictic 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)
marscan  Finds matrix/scaffold recognition (MRS) signatures in DNA sequences

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

NUCLEIC PRIMERS
eprimer3     Picks 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 REPEATS
einverted    Finds inverted repeats in nucleotide sequences
equicktandem Finds tandem repeats in nucleotide sequences
etandem      Finds tandem repeats in a nucleotide sequence
palindrome   Finds 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  Displays sequences with features in pretty format
silent   Find restriction sites to insert (mutate) with no translation change

NUCLEIC RNA FOLDING
vrnaalifold    RNA alignment folding
vrnaalifoldpf  RNA alignment folding with partition
vrnacofold     RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf   RNA cofolding with partitioning
vrnadistance   RNA distances
vrnaduplex     RNA duplex calculation
vrnaeval       RNA eval
vrnaevalpair   RNA eval with cofold
vrnafold       Calculate secondary structures of RNAs
vrnafoldpf     Secondary structures of RNAs with partition
vrnaheat       RNA melting
vrnainverse    RNA sequences matching a structure
vrnalfold      Calculate locally stable secondary structures of RNAs
vrnaplot       Plot vrnafold output
vrnasubopt     Calculate RNA suboptimals

NUCLEIC TRANSCRIPTION
jaspscan Scans DNA sequences for transcription factors
tfscan   Identify transcription factor binding sites in DNA sequences

NUCLEIC TRANSLATION
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequenc
e
backtranseq   Back-translate a protein sequence to a nucleotide sequence
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       Displays sequences with features in pretty format
sixpack       Display a DNA sequence with 6-frame translation and ORFs
transeq       Translate nucleic acid sequences

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

PHYLOGENY CONTINUOUS CHARACTERS
econtml   Continuous character Maximum Likelihood method
econtrast Continuous character Contrasts
fcontrast Continuous character Contrasts

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

PHYLOGENY DISTANCE MATRIX
efitch    Fitch-Margoliash and Least-Squares Distance Methods
ekitsch   Fitch-Margoliash method with contemporary tips
eneighbor Phylogenies from distance matrix by N-J or UPGMA method
ffitch    Fitch-Margoliash and Least-Squares Distance Methods
fkitsch   Fitch-Margoliash method with contemporary tips
fneighbor Phylogenies from distance matrix by N-J or UPGMA method

PHYLOGENY GENE FREQUENCIES
egendist Genetic Distance Matrix program
fcontml  Gene frequency and continuous character Maximum Likelihood
fgendist Compute genetic distances from gene frequencies

PHYLOGENY MOLECULAR SEQUENCE
distmat     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      Estimates nucleotide phylogeny by maximum likelihood
fdnamlk     Estimates nucleotide phylogeny by maximum likelihood
fdnamove    Interactive DNA parsimony
fdnapars    DNA parsimony algorithm
fdnapenny   Penny algorithm for DNA
fdolmove    Interactive Dollo or Polymorphism Parsimony
ffreqboot   Bootstrapped genetic frequencies algorithm
fproml      Protein phylogeny by maximum likelihood
fpromlk     Protein phylogeny by maximum likelihood
fprotdist   Protein distance algorithm
fprotpars   Protein parsimony algorithm
frestboot   Bootstrapped restriction sites algorithm
frestdist   Distance matrix from restriction sites or fragments
frestml     Restriction site maximum Likelihood method
fseqboot    Bootstrapped sequences algorithm
fseqbootall Bootstrapped sequences algorithm

PHYLOGENY TREE DRAWING
fdrawgram Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree Plots an unrooted tree diagram
fretree   Interactive tree rearrangement

PROTEIN 2D STRUCTURE
garnier        Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hmoment        Calculate and plot hydrophobic moment for protein sequence(s)
pepcoil        Predicts 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
tmap           Predict and plot transmembrane segments in protein sequences
topo           Draws an image of a transmembrane protein

PROTEIN 3D STRUCTURE
contacts    Generate intra-chain CON files from CCF files
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainrep   Reorder DCF file to identify representative structures
domainreso  Remove low resolution domains from a DCF file
interface   Generate inter-chain CON files from CCF files
libgen      Generate discriminating elements from alignments
matgen3d    Generate a 3D-1D scoring matrix from CCF files
psiphi      Calculates phi and psi torsion angles from protein coordinates
rocon       Generates a hits file from comparing two DHF files
rocplot     Performs ROC analysis on hits files
seqalign    Extend alignments (DAF file) with sequences (DHF file)
seqfraggle  Removes fragment sequences from DHF files
seqsearch   Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort     Remove ambiguous classified sequences from DHF files
seqwords    Generates DHF files from keyword search of UniProt
siggen      Generates a sparse protein signature from an alignment
siggenlig   Generates ligand-binding signatures from a CON file
sigscan     Generates hits (DHF file) from a signature search
sigscanlig  Searches ligand-signature library & writes hits (LHF file)

PROTEIN COMPOSITION
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequenc
e
backtranseq   Back-translate a protein sequence to a nucleotide sequence
charge        Draw a protein charge plot
checktrans    Reports STOP codons and ORF statistics of a protein
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
iep           Calculate the isoelectric point of proteins
mwcontam      Find weights common to multiple molecular weights files
mwfilter      Filter noisy data from molecular weights file
octanol       Draw a White-Wimley protein hydropathy plot
pepinfo       Plot amino acid properties of a protein sequence in parallel
pepstats      Calculates statistics of protein properties
pepwindow     Draw a hydropathy plot for a protein sequence
pepwindowall  Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount     Count and extract unique words in DNA sequence(s)

PROTEIN MOTIFS
antigenic      Finds antigenic sites in proteins
digest         Reports on protein proteolytic enzyme or reagent cleavage sites
echlorop       Reports presence of chloroplast transit peptides
eiprscan       Motif detection
elipop         Prediction of lipoproteins
emast          Motif detection
ememe          Multiple EM for Motif Elicitation
ememetext      Multiple EM for Motif Elicitation. Text file only
enetnglyc      Reports N-glycosylation sites in human proteins
enetoglyc      Reports mucin type GalNAc O-glycosylation sites in mammalian pro
teins
enetphos       Reports ser, thr and tyr phosphorylation sites in eukaryotic pro
teins
epestfind      Finds PEST motifs as potential proteolytic cleavage sites
eprop          Reports propeptide cleavage sites in proteins
esignalp       Reports protein signal cleavage sites
etmhmm         Reports transmembrane helices
eyinoyang      Reports O-(beta)-GlcNAc attachment sites
fuzzpro        Search for patterns in protein sequences
fuzztran       Search for patterns in protein sequences (translated)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
oddcomp        Identify proteins with specified sequence word composition
omeme          Motif detection
patmatdb       Searches protein sequences with a sequence motif
patmatmotifs   Scan a protein sequence with motifs from the PROSITE database
pepcoil        Predicts coiled coil regions in protein sequences
preg           Regular expression search of protein sequence(s)
pscan          Scans protein sequence(s) with fingerprints from the PRINTS data
base
sigcleave      Reports on signal cleavage sites in a protein sequence

PROTEIN MUTATION
msbar      Mutate a sequence
shuffleseq Shuffles 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

TEST
crystalball Answers every drug discovery question about a sequence

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

UTILS MISC
embossdata    Find and retrieve EMBOSS data files
embossversion Reports the current EMBOSS version number


   Example 3

   Display an alphabetic listing of all programs:


% wossname -search '' -alphabetic 
Finds 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 fil
e
acdtrace       Trace processing of an application ACD file (for testing)
acdvalid       Validate an application ACD file
aligncopy      Reads and writes alignments
aligncopypair  Reads and writes pairs from alignments
allversusall   Sequence similarity data from all-versus-all comparison
antigenic      Finds antigenic sites in proteins
backtranambig  Back-translate a protein sequence to ambiguous nucleotide sequen
ce
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
cai            Calculate codon adaptation index
cathparse      Generates DCF file from raw CATH files
chaos          Draw a chaos game representation plot for a nucleotide sequence
charge         Draw a protein charge plot
checktrans     Reports STOP codons and ORF statistics of a protein
chips          Calculates Nc codon usage statistic
cirdna         Draws circular maps 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 alignment
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    Answers every drug discovery question about a sequence
cusp           Create a codon usage table from nucleotide sequence(s)
cutgextract    Extract codon usage tables from from CUTG database
cutseq         Removes a section from a sequence
dan            Calculates 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
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
degapseq       Removes 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
digest         Reports on protein proteolytic enzyme or reagent cleavage sites
distmat        Create a distance matrix from a multiple sequence alignment
domainalign    Generate alignments (DAF file) for nodes in a DCF file
domainer       Generates domain CCF files from protein CCF files
domainnr       Removes redundant domains from a DCF file
domainrep      Reorder DCF file to identify representative structures
domainreso     Remove low resolution domains from a DCF file
domainseqs     Adds sequence records to a DCF file
domainsse      Add secondary structure records to a DCF file
dotmatcher     Draw a threshold dotplot of two sequences
dotpath        Draw a non-overlapping wordmatch dotplot of two sequences
dottup         Displays a wordmatch dotplot of two sequences
dreg           Regular expression search of nucleotide sequence(s)
echlorop       Reports 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
edialign       Local multiple alignment of sequences
ednacomp       DNA compatibility algorithm
ednadist       Nucleic acid sequence Distance Matrix program
ednainvar      Nucleic acid sequence Invariants method
ednaml         Phylogenies from nucleic acid Maximum Likelihood
ednamlk        Phylogenies from nucleic acid Maximum Likelihood with clock
ednapars       DNA parsimony algorithm
ednapenny      Penny algorithm for DNA
edollop        Dollo and polymorphism parsimony algorithm
edolpenny      Penny algorithm Dollo or polymorphism
efactor        Multistate to binary recoding program
efitch         Fitch-Margoliash and Least-Squares Distance Methods
egendist       Genetic Distance Matrix program
ehmmalign      Align sequences to an HMM profile
ehmmbuild      Build a profile HMM from an alignment
ehmmcalibrate  Calibrate HMM search statistics
ehmmconvert    Convert between profile HMM file formats
ehmmemit       Generate sequences from a profile HMM
ehmmfetch      Retrieve an HMM from an HMM database
ehmmindex      Create a binary SSI index for an HMM database
ehmmpfam       Search one or more sequences against an HMM database
ehmmsearch     Search a sequence database with a profile HMM
einverted      Finds inverted repeats in nucleotide sequences
eiprscan       Motif detection
ekitsch        Fitch-Margoliash method with contemporary tips
elipop         Prediction of lipoproteins
emast          Motif detection
embossdata     Find and retrieve EMBOSS data files
embossversion  Reports 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      Reports N-glycosylation sites in human proteins
enetoglyc      Reports mucin type GalNAc O-glycosylation sites in mammalian pro
teins
enetphos       Reports ser, thr and tyr phosphorylation sites in eukaryotic pro
teins
entret         Retrieves sequence entries from flatfile databases and files
epenny         Penny algorithm, branch-and-bound
epestfind      Finds PEST motifs as potential proteolytic cleavage sites
eprimer3       Picks PCR primers and hybridization oligos
eprop          Reports propeptide cleavage sites in proteins
eprotdist      Protein distance algorithm
eprotpars      Protein parsimony algorithm
equicktandem   Finds tandem repeats in nucleotide sequences
erestml        Restriction site Maximum Likelihood method
eseqboot       Bootstrapped sequences algorithm
esignalp       Reports protein signal cleavage sites
esim4          Align an mRNA to a genomic DNA sequence
est2genome     Align EST sequences to genomic DNA sequence
etandem        Finds 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      Reports 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         Estimates nucleotide phylogeny by maximum likelihood
fdnamlk        Estimates nucleotide phylogeny by maximum likelihood
fdnamove       Interactive DNA parsimony
fdnapars       DNA parsimony algorithm
fdnapenny      Penny algorithm for DNA
fdollop        Dollo and polymorphism parsimony algorithm
fdolmove       Interactive Dollo or Polymorphism Parsimony
fdolpenny      Penny algorithm Dollo or polymorphism
fdrawgram      Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree      Plots an unrooted tree diagram
featcopy       Reads and writes a feature table
featreport     Reads and writes a feature table
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      Distance matrix from restriction sites or fragments
frestml        Restriction site maximum Likelihood method
fretree        Interactive tree rearrangement
fseqboot       Bootstrapped sequences algorithm
fseqbootall    Bootstrapped sequences algorithm
ftreedist      Distances between trees
ftreedistpair  Distances between two sets of trees
fuzznuc        Search for patterns in nucleotide sequences
fuzzpro        Search for patterns in protein sequences
fuzztran       Search for patterns in protein sequences (translated)
garnier        Predicts protein secondary structure using GOR method
geecee         Calculate fractional GC content of nucleic acid sequences
getorf         Finds and extracts open reading frames (ORFs)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hetparse       Converts 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
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       Plots isochores in DNA sequences
jaspextract    Extract data from JASPAR
jaspscan       Scans DNA sequences for transcription factors
libgen         Generate discriminating elements from alignments
lindna         Draws linear maps of DNA constructs
listor         Write a list file of the logical OR of two sets of sequences
makenucseq     Create random nucleotide sequences
makeprotseq    Create random protein sequences
marscan        Finds matrix/scaffold recognition (MRS) signatures in DNA sequen
ces
maskambignuc   Masks all ambiguity characters in nucleotide sequences with N
maskambigprot  Masks 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
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 all 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 sequence
s
nthseqset      Reads and writes (returns) 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
palindrome     Finds inverted repeats in nucleotide sequence(s)
pasteseq       Insert one sequence into another
patmatdb       Searches protein sequences with a sequence motif
patmatmotifs   Scan a protein sequence with motifs from the PROSITE database
pdbparse       Parses PDB files and writes protein CCF files
pdbplus        Add accessibility & secondary structure to a CCF file
pdbtosp        Convert swissprot:PDB codes file to EMBL-like format
pepcoil        Predicts coiled coil regions in protein sequences
pepinfo        Plot amino acid properties of a protein sequence in parallel
pepnet         Draw a helical net for a protein sequence
pepstats       Calculates 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    Processes the PROSITE motif database for use by patmatmotifs
pscan          Scans 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 applic
ations
recoder        Find restriction sites to remove (mutate) with no translation ch
ange
redata         Retrieve information from REBASE restriction enzyme database
remap          Display restriction enzyme binding sites in a nucleotide sequenc
e
restover       Find restriction enzymes producing a specific overhang
restrict       Report restriction enzyme cleavage sites in a nucleotide sequenc
e
revseq         Reverse and complement a nucleotide sequence
rocon          Generates a hits file from comparing two DHF files
rocplot        Performs ROC analysis on hits files
scopparse      Generate DCF file from raw SCOP files
seealso        Finds programs with similar function to a specified program
seqalign       Extend alignments (DAF file) with sequences (DHF file)
seqfraggle     Removes fragment sequences from DHF files
seqmatchall    All-against-all word comparison of a sequence set
seqnr          Removes redundancy from DHF files
seqret         Reads and writes (returns) sequences
seqretsetall   Reads and writes (returns) many sets of sequences
seqretsplit    Reads sequences and writes them to individual files
seqsearch      Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort        Remove ambiguous classified sequences from DHF files
seqwords       Generates DHF files from keyword search of UniProt
showalign      Display a multiple sequence alignment in pretty format
showdb         Displays information on configured databases
showfeat       Display features of a sequence in pretty format
showorf        Display a nucleotide sequence and translation in pretty format
showpep        Displays protein sequences with features in pretty format
showseq        Displays sequences with features in pretty format
shuffleseq     Shuffles a set of sequences maintaining composition
sigcleave      Reports on signal cleavage sites in a protein sequence
siggen         Generates a sparse protein signature from an alignment
siggenlig      Generates ligand-binding signatures from a CON file
sigscan        Generates hits (DHF file) from a signature search
sigscanlig     Searches ligand-signature library & writes hits (LHF file)
silent         Find restriction sites to insert (mutate) with no translation ch
ange
sirna          Finds siRNA duplexes in mRNA
sites          Generate residue-ligand CON files from CCF files
sixpack        Display a DNA sequence with 6-frame translation and ORFs
sizeseq        Sort sequences by size
skipredundant  Remove redundant sequences from an input set
skipseq        Reads and writes (returns) 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 seque
nces
syco           Draw synonymous codon usage statictic plot for a nucleotide sequ
ence
tcode          Identify protein-coding regions using Fickett TESTCODE statistic
textsearch     Search the textual description of sequence(s)
tfextract      Process TRANSFAC transcription factor database for use by tfscan
tfm            Displays full documentation for an application
tfscan         Identify transcription factor binding sites in DNA sequences
tmap           Predict and plot transmembrane segments in protein sequences
topo           Draws an image of a transmembrane protein
tranalign      Generate an alignment of nucleic coding regions from aligned pro
teins
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        Finds neighbouring pairs of features in sequence(s)
union          Concatenate multiple sequences into a single sequence
vectorstrip    Removes vectors from the ends of nucleotide sequence(s)
vrnaalifold    RNA alignment folding
vrnaalifoldpf  RNA alignment folding with partition
vrnacofold     RNA cofolding
vrnacofoldconc RNA cofolding with concentrations
vrnacofoldpf   RNA cofolding with partitioning
vrnadistance   RNA distances
vrnaduplex     RNA duplex calculation
vrnaeval       RNA eval
vrnaevalpair   RNA eval with cofold
vrnafold       Calculate secondary structures of RNAs
vrnafoldpf     Secondary structures of RNAs with partition
vrnaheat       RNA melting
vrnainverse    RNA sequences matching a structure
vrnalfold      Calculate locally stable secondary structures of RNAs
vrnaplot       Plot vrnafold output
vrnasubopt     Calculate RNA suboptimals
water          Smith-Waterman local alignment 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 DNA sequence(s)
wordfinder     Match large sequences against one or more other sequences
wordmatch      Finds regions of identity (exact matches) of two sequences
wossname       Finds programs by keywords in their short description
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 
Finds programs by keywords in their short description

ACD
ALIGNMENT CONSENSUS
ALIGNMENT DIFFERENCES
ALIGNMENT DOT PLOTS
ALIGNMENT GLOBAL
ALIGNMENT LOCAL
ALIGNMENT MULTIPLE
ASSEMBLY FRAGMENT ASSEMBLY
DISPLAY
EDIT
ENZYME KINETICS
FEATURE TABLES
HMM
INFORMATION
MENUS
NUCLEIC 2D STRUCTURE
NUCLEIC CODON USAGE
NUCLEIC COMPOSITION
NUCLEIC CPG ISLANDS
NUCLEIC GENE FINDING
NUCLEIC MOTIFS
NUCLEIC MUTATION
NUCLEIC PRIMERS
NUCLEIC PROFILES
NUCLEIC REPEATS
NUCLEIC RESTRICTION
NUCLEIC RNA FOLDING
NUCLEIC TRANSCRIPTION
NUCLEIC TRANSLATION
PHYLOGENY CONSENSUS
PHYLOGENY CONTINUOUS CHARACTERS
PHYLOGENY DISCRETE CHARACTERS
PHYLOGENY DISTANCE MATRIX
PHYLOGENY GENE FREQUENCIES
PHYLOGENY MOLECULAR SEQUENCE
PHYLOGENY TREE DRAWING
PROTEIN 2D STRUCTURE
PROTEIN 3D STRUCTURE
PROTEIN COMPOSITION
PROTEIN MOTIFS
PROTEIN MUTATION
PROTEIN PROFILES
TEST
UTILS DATABASE CREATION
UTILS DATABASE INDEXING
UTILS MISC

   Example 5

   Output html tags around the list of programs:


% wossname '' -html -out wossname.html 
Finds programs by keywords in their short description

   Go to the output files for this example

Command line arguments

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

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

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

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write 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. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

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

   The format of ACD files is documented elsewhere.

Output file format

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

  Output files for usage example 5

  File: wossname.html

   

ACD

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

ALIGNMENT CONSENSUS

[Part of this file has been deleted for brevity]
Program name Description
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
dbiblast Index a BLAST database
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
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

UTILS MISC

Program name Description
embossdata Find and retrieve EMBOSS data files
embossversion Reports the current EMBOSS version number
If the -html, -prelink and -postlink qualifiers are specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as , , and are not output by this program as the list of programs is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user. Data files As noted above, the program ACD files are searched. The average user will not need to worry about this. Notes 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 infoalign Display basic information about a multiple sequence alignment infobase Return information on a given nucleotide base inforesidue Return information on a given amino acid residue infoseq Display basic information about sequences seealso Finds programs with similar function to a specified program showdb Displays information on configured databases textsearch Search the textual description of sequence(s) tfm Displays full documentation for an application whichdb Search all sequence databases for an entry and retrieve it Author(s) Gary Williams (gwilliam rfcgr.mrc.ac.uk) MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None

Command line arguments

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

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

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

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write 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. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-program]
(Parameter 1)
Enter the name of an EMBOSS program Any string of at least 1 characters Required
Additional (Optional) qualifiers Allowed values Default
-outfile Program documentation text output file Output file stdout
-html This will format the output for displaying as a WWW document. Boolean value Yes/No No
-more This uses the standard UNIX utility 'more' to display the text page-by-page, waiting for you to read one screen-full before going on to the next page. When you have finished reading a page, press the SPACE bar to proceed to the next page. Boolean value Yes/No @(!$(html))
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

None.

Output file format

Text documentation is output.

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

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

Data files

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

Notes

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

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

Paged text output to the screen

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

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

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

References

None.

Warnings

None.

Diagnostic Error Messages

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

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
infoalign Display basic information about a multiple sequence alignment
infobase Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue
infoseq Display basic information about sequences
seealso Finds programs with similar function to a specified program
showdb Displays information on configured databases
textsearch Search the textual description of sequence(s)
whichdb Search all sequence databases for an entry and retrieve it
wossname Finds programs by keywords in their short description

Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Written: 4 Aug 2000.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None