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     Displays a wordmatch dotplot of two sequences
polydot    Draw dotplots for all-against-all comparison of a sequence set

ALIGNMENT GLOBAL
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
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 sequences
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
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

ASSORTED
[      

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

DATA RETRIEVAL
codcopy Copy and reformat a codon usage table
seqret  Reads and writes (returns) 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 Reads and writes a feature table

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       Retrieves 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
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
whichdb      Search all sequence databases for an entry and retrieve it

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

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

DATA RETRIEVAL URL DATA
urlget Get URLs of data resources

DISPLAY
abiview    Display the trace in an ABI sequencer file
cirdna     Draws circular maps of DNA constructs
iep        Calculate the isoelectric point of proteins
lindna     Draws 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    Displays protein sequences with features in pretty format
sixpack    Display a DNA sequence with 6-frame translation and ORFs

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

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
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  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 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
seqcount      Reads and counts sequences
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
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)

NUCLEIC 2D STRUCTURE
banana    Plot bending and curvature data for B-DNA
btwisted  Calculate the twisting in a B-DNA sequence
einverted Finds inverted repeats in nucleotide sequences
sirna     Finds siRNA duplexes in mRNA

NUCLEIC CODON USAGE
cai     Calculate codon adaptation index
chips   Calculates 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       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
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 Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
sirna   Finds siRNA duplexes in mRNA
trimest Remove poly-A tails from nucleotide sequences

NUCLEIC GENE FINDING
checktrans Reports STOP codons and ORF statistics of a protein
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 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 Shuffles a set of sequences maintaining composition

NUCLEIC PRIMERS
eprimer3     Picks PCR primers and hybridization oligos
eprimer32    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 PROPERTIES
banana   Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
dan      Calculates nucleic acid melting temperature

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 TRANSCRIPTION
jaspscan Scans DNA sequences for transcription factors
marscan  Finds 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    Reports 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       Displays 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       Finds programs by EDAM data
wossinput      Finds programs by EDAM input data
wossoperation  Finds programs by EDAM operation
wossoutput     Finds programs by EDAM output data
wossparam      Finds programs by EDAM parameter
wosstopic      Finds 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 MOLECULAR SEQUENCE
distmat Create a distance matrix from a multiple sequence alignment

PROTEIN 2D STRUCTURE
garnier        Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
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

PROTEIN 3D STRUCTURE
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     Reports on protein proteolytic enzyme or reagent cleavage sites
pepinfo       Plot amino acid properties of a protein sequence in parallel
pepstats      Calculates statistics of protein properties
wordcount     Count and extract unique words in molecular sequence(s)

PROTEIN DOMAINS
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
pepcoil        Predicts coiled coil regions in protein sequences

PROTEIN FUNCTIONAL SITES
sigcleave Reports on signal cleavage sites in a protein sequence
tmap      Predict and plot transmembrane segments in protein sequences

PROTEIN MOTIFS
antigenic    Finds antigenic sites in proteins
epestfind    Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro      Search for patterns in protein sequences
fuzztran     Search for patterns in protein sequences (translated)
patmatdb     Searches 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        Scans protein sequence(s) with fingerprints from the PRINTS database
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

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     Calculates statistics of protein properties
pepwindow    Draw a hydropathy plot for a protein sequence
pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein alignment

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

UTILS DATABASE CREATION
aaindexextract Extract amino acid property data from AAINDEX
cutgextract    Extract codon usage tables from CUTG database
jaspextract    Extract data from JASPAR
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 applications
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

