abiview         Display the trace in an ABI sequencer file
aligncopy       Read and write alignments
aligncopypair   Read and write pairs from alignments
antigenic       Find 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
cai             Calculate codon adaptation index
chaos           Draw a chaos game representation plot for a nucleotide sequence
charge          Draw a protein charge plot
checktrans      Report STOP codons and ORF statistics of a protein
chips           Calculate Nc codon usage statistic
cirdna          Draw circular map of DNA constructs
codcmp          Codon usage table comparison
codcopy         Copy and reformat a codon usage table
coderet         Extract CDS, mRNA and translations from feature tables
compseq         Calculate the composition of unique words in sequences
cons            Create a consensus sequence from a multiple alignment
consambig       Create an ambiguous consensus sequence from a multiple 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)
cutseq          Remove a section from a sequence
dan             Calculate nucleic acid melting temperature
dbtell          Display information about a public database
degapseq        Remove non-alphabetic (e.g. gap) characters from sequences
density         Draw a nucleic acid density plot
descseq         Alter the name or description of a sequence
diffseq         Compare and report features of two similar sequences
distmat         Create a distance matrix from a multiple sequence alignment
dotmatcher      Draw a threshold dotplot of two sequences
dotpath         Draw a non-overlapping wordmatch dotplot of two sequences
dottup          Display a wordmatch dotplot of two sequences
dreg            Regular expression search of nucleotide sequence(s)
drfinddata      Find public databases by data type
drfindformat    Find public databases by format
drfindid        Find public databases by identifier
drfindresource  Find public databases by resource
drget           Get data resource entries
drtext          Get data resource entries complete text
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       Find inverted repeats in nucleotide sequences
emma            Multiple sequence alignment (ClustalW wrapper)
emowse          Search protein sequences by digest fragment molecular weight
entret          Retrieve sequence entries from flatfile databases and files
epestfind       Find PEST motifs as potential proteolytic cleavage sites
eprimer3        Pick PCR primers and hybridization oligos
eprimer32       Pick PCR primers and hybridization oligos
equicktandem    Find tandem repeats in nucleotide sequences
est2genome      Align EST sequences to genomic DNA sequence
etandem         Find 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        Read and write a feature table
featreport      Read and write 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         Predict protein secondary structure using GOR method
geecee          Calculate fractional GC content of nucleic acid sequences
getorf          Find and extract open reading frames (ORFs)
godef           Find GO ontology terms by definition
goname          Find GO ontology terms by name
helixturnhelix  Identify nucleic acid-binding motifs in protein sequences
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        Plot isochores in DNA sequences
jaspscan        Scan DNA sequences for transcription factors
lindna          Draw linear maps of DNA constructs
listor          Write a list file of the logical OR of two sets of sequences
makenucseq      Create random nucleotide sequences
makeprotseq     Create random protein sequences
marscan         Find matrix/scaffold recognition (MRS) signatures in DNA sequences
maskambignuc    Mask all ambiguity characters in nucleotide sequences with N
maskambigprot   Mask all ambiguity characters in protein sequences with X
maskfeat        Write a sequence with masked features
maskseq         Write a sequence with masked regions
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       Read and write (return) 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      Find inverted repeats in nucleotide sequence(s)
pasteseq        Insert one sequence into another
patmatdb        Search protein sequences with a sequence motif
patmatmotifs    Scan a protein sequence with motifs from the PROSITE database
pepcoil         Predict coiled coil regions in protein sequences
pepdigest       Report on protein proteolytic enzyme or reagent cleavage sites
pepinfo         Plot amino acid properties of a protein sequence in parallel
pepnet          Draw a helical net for a protein sequence
pepstats        Calculate statistics of protein properties
pepwheel        Draw a helical wheel diagram for a protein sequence
pepwindow       Draw a hydropathy plot for a protein sequence
pepwindowall    Draw Kyte-Doolittle hydropathy plot for a protein alignment
plotcon         Plot conservation of a sequence alignment
plotorf         Plot potential open reading frames in a nucleotide sequence
polydot         Draw dotplots for all-against-all comparison of a sequence set
preg            Regular expression search of protein sequence(s)
prettyplot      Draw a sequence alignment with pretty formatting
prettyseq       Write a nucleotide sequence and its translation to file
primersearch    Search DNA sequences for matches with primer pairs
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
pscan           Scan protein sequence(s) with fingerprints from the PRINTS database
psiphi          Calculates phi and psi torsion angles from protein coordinates
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
seqcount        Read and count sequences
seqmatchall     All-against-all word comparison of a sequence set
seqret          Read and write (return) sequences
seqretsetall    Read and write (return) many sets of sequences
seqretsplit     Read sequences and write them to individual files
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
showfeat        Display features of a sequence in pretty format
showorf         Display a nucleotide sequence and translation in pretty format
showpep         Display protein sequences with features in pretty format
showseq         Display sequences with features in pretty format
shuffleseq      Shuffle a set of sequences maintaining composition
sigcleave       Report on signal cleavage sites in a protein sequence
silent          Find restriction sites to insert (mutate) with no translation change
sirna           Find 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         Read and write (return) 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)
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         Find neighbouring pairs of features in sequence(s)
union           Concatenate multiple sequences into a single sequence
urlget          Get URLs of data resources
vectorstrip     Remove 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       Find regions of identity (exact matches) of two sequences
xmlget           Get XML data
xmltext          Get XML document original full text
