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 file
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
antigenic        Finds antigenic sites in proteins
backtranambig    Back-translate a protein sequence to ambiguous nucleotide sequence
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         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
cai              Calculate codon adaptation index
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
cpgplot          Identify and plot CpG islands in nucleotide sequence(s)
cpgreport        Identify and report CpG-rich regions in nucleotide sequence(s)
cusp             Create a codon usage table from nucleotide sequence(s)
cutgextract      Extract codon usage tables 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
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         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
distmat          Create a distance matrix from a multiple sequence alignment
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)
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
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
einverted        Finds inverted repeats in nucleotide sequences
embossdata       Find and retrieve EMBOSS data files
embossversion    Reports the current EMBOSS version number
emma             Multiple sequence alignment (ClustalW wrapper)
emowse           Search protein sequences by digest fragment molecular weight
entret           Retrieves sequence entries from flatfile databases and files
epestfind        Finds PEST motifs as potential proteolytic cleavage sites
eprimer3         Picks PCR primers and hybridization oligos
eprimer32        Picks PCR primers and hybridization oligos
equicktandem     Finds tandem repeats in nucleotide sequences
est2genome       Align EST sequences to genomic DNA sequence
etandem          Finds tandem repeats in a nucleotide sequence
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
findkm           Calculate and plot enzyme reaction data
freak            Generate residue/base frequency table or plot
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)
godef            Find GO ontology terms by definition
goname           Find GO ontology terms by name
helixturnhelix   Identify nucleic acid-binding motifs in protein sequences
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
isochore         Plots isochores in DNA sequences
jaspextract      Extract data from JASPAR
jaspscan         Scans DNA sequences for transcription factors
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 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
matcher          Waterman-Eggert local alignment of two sequences
megamerger       Merge two large overlapping DNA sequences
merger           Merge two overlapping sequences
msbar            Mutate a sequence
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 sequences
nthseqset        Reads and writes (returns) one set of sequences from many
octanol          Draw a White-Wimley protein hydropathy plot
oddcomp          Identify proteins with specified sequence word composition
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
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
pepcoil          Predicts coiled coil regions in protein sequences
pepdigest        Reports 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         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 database
psiphi           Calculates phi and psi torsion angles from protein coordinates
rebaseextract    Process the REBASE database for use by restriction enzyme applications
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
revseq           Reverse and complement a nucleotide sequence
seealso          Finds programs with similar function to a specified program
seqcount         Reads and counts sequences
seqmatchall      All-against-all word comparison of a sequence set
seqret           Reads and writes (returns) sequences
seqretsetall     Reads and writes (returns) many sets of sequences
seqretsplit      Reads sequences and writes them to individual files
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           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
showserver       Displays information on configured servers
shuffleseq       Shuffles a set of sequences maintaining composition
sigcleave        Reports on signal cleavage sites in a protein sequence
silent           Find restriction sites to insert (mutate) with no translation change
sirna            Finds siRNA duplexes in mRNA
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
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 sequences
syco             Draw synonymous codon usage statistic plot for a nucleotide sequence
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 statistic
textget          Get text data entries
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
tranalign        Generate an alignment of nucleic coding regions from aligned proteins
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
urlget           Get URLs of data resources
vectorstrip      Removes vectors from the ends of nucleotide sequence(s)
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        Finds regions of identity (exact matches) of two sequences
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
yank             Add a sequence reference (a full USA) to a list file
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