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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: The Applications (programs)
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">



<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="http://emboss.sourceforge.net/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true">
<img border=0 src="/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6"> 
The Applications (programs)
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>




The programs are listed in alphabetical order, Look at the individual
applications or go to the 
<a href="groups.html">GROUPS</a>
page to search by category. 
<p>

<a href="../../embassy/index.html">EMBASSY applications</a>
are described in separate documentation for each package.

<h3><A NAME="current">Applications</A> in the <a
href="ftp://emboss.open-bio.org/pub/EMBOSS/">current release</a></h3>

<table border cellpadding=4 bgcolor="#FFFFF0">

<tr>
<th>Program name</th>
<th>Description</th>
</tr>

<tr>
<td><a href="aaindexextract.html">aaindexextract</a></td>
<td>
Extract amino acid property data from AAINDEX
</td>
</tr>
<tr>
<td><a href="abiview.html">abiview</a></td>
<td>
Display the trace in an ABI sequencer file
</td>
</tr>
<tr>
<td><a href="acdc.html">acdc</a></td>
<td>
Test an application ACD file
</td>
</tr>
<tr>
<td><a href="acdpretty.html">acdpretty</a></td>
<td>
Correctly reformat an application ACD file
</td>
</tr>
<tr>
<td><a href="acdtable.html">acdtable</a></td>
<td>
Generate an HTML table of parameters from an application ACD file
</td>
</tr>
<tr>
<td><a href="acdtrace.html">acdtrace</a></td>
<td>
Trace processing of an application ACD file (for testing)
</td>
</tr>
<tr>
<td><a href="acdvalid.html">acdvalid</a></td>
<td>
Validate an application ACD file
</td>
</tr>
<tr>
<td><a href="aligncopy.html">aligncopy</a></td>
<td>
Read and write alignments
</td>
</tr>
<tr>
<td><a href="aligncopypair.html">aligncopypair</a></td>
<td>
Read and write pairs from alignments
</td>
</tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>
Find antigenic sites in proteins
</td>
</tr>
<tr>
<td><a href="assemblyget.html">assemblyget</a></td>
<td>
Get assembly of sequence reads
</td>
</tr>
<tr>
<td><a href="backtranambig.html">backtranambig</a></td>
<td>
Back-translate a protein sequence to ambiguous nucleotide sequence
</td>
</tr>
<tr>
<td><a href="backtranseq.html">backtranseq</a></td>
<td>
Back-translate a protein sequence to a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="banana.html">banana</a></td>
<td>
Plot bending and curvature data for B-DNA
</td>
</tr>
<tr>
<td><a href="biosed.html">biosed</a></td>
<td>
Replace or delete sequence sections
</td>
</tr>
<tr>
<td><a href="btwisted.html">btwisted</a></td>
<td>
Calculate the twisting in a B-DNA sequence
</td>
</tr>
<tr>
<td><a href="cachedas.html">cachedas</a></td>
<td>
Generate server cache file for DAS servers or for the DAS registry
</td>
</tr>
<tr>
<td><a href="cachedbfetch.html">cachedbfetch</a></td>
<td>
Generate server cache file for Dbfetch/WSDbfetch data sources
</td>
</tr>
<tr>
<td><a href="cacheebeyesearch.html">cacheebeyesearch</a></td>
<td>
Generate server cache file for EB-eye search domains
</td>
</tr>
<tr>
<td><a href="cacheensembl.html">cacheensembl</a></td>
<td>
Generate server cache file for an Ensembl server
</td>
</tr>
<tr>
<td><a href="cai.html">cai</a></td>
<td>
Calculate codon adaptation index
</td>
</tr>
<tr>
<td><a href="chaos.html">chaos</a></td>
<td>
Draw a chaos game representation plot for a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="charge.html">charge</a></td>
<td>
Draw a protein charge plot
</td>
</tr>
<tr>
<td><a href="checktrans.html">checktrans</a></td>
<td>
Report STOP codons and ORF statistics of a protein
</td>
</tr>
<tr>
<td><a href="chips.html">chips</a></td>
<td>
Calculate Nc codon usage statistic
</td>
</tr>
<tr>
<td><a href="cirdna.html">cirdna</a></td>
<td>
Draw circular map of DNA constructs
</td>
</tr>
<tr>
<td><a href="codcmp.html">codcmp</a></td>
<td>
Codon usage table comparison
</td>
</tr>
<tr>
<td><a href="codcopy.html">codcopy</a></td>
<td>
Copy and reformat a codon usage table
</td>
</tr>
<tr>
<td><a href="coderet.html">coderet</a></td>
<td>
Extract CDS, mRNA and translations from feature tables
</td>
</tr>
<tr>
<td><a href="compseq.html">compseq</a></td>
<td>
Calculate the composition of unique words in sequences
</td>
</tr>
<tr>
<td><a href="cons.html">cons</a></td>
<td>
Create a consensus sequence from a multiple alignment
</td>
</tr>
<tr>
<td><a href="consambig.html">consambig</a></td>
<td>
Create an ambiguous consensus sequence from a multiple alignment
</td>
</tr>
<tr>
<td><a href="cpgplot.html">cpgplot</a></td>
<td>
Identify and plot CpG islands in nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="cpgreport.html">cpgreport</a></td>
<td>
Identify and report CpG-rich regions in nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="cusp.html">cusp</a></td>
<td>
Create a codon usage table from nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="cutgextract.html">cutgextract</a></td>
<td>
Extract codon usage tables from CUTG database
</td>
</tr>
<tr>
<td><a href="cutseq.html">cutseq</a></td>
<td>
Remove a section from a sequence
</td>
</tr>
<tr>
<td><a href="dan.html">dan</a></td>
<td>
Calculate nucleic acid melting temperature
</td>
</tr>
<tr>
<td><a href="dbiblast.html">dbiblast</a></td>
<td>
Index a BLAST database
</td>
</tr>
<tr>
<td><a href="dbifasta.html">dbifasta</a></td>
<td>
Index a fasta file database
</td>
</tr>
<tr>
<td><a href="dbiflat.html">dbiflat</a></td>
<td>
Index a flat file database
</td>
</tr>
<tr>
<td><a href="dbigcg.html">dbigcg</a></td>
<td>
Index a GCG formatted database
</td>
</tr>
<tr>
<td><a href="dbtell.html">dbtell</a></td>
<td>
Display information about a public database
</td>
</tr>
<tr>
<td><a href="dbxcompress.html">dbxcompress</a></td>
<td>
Compress an uncompressed dbx index
</td>
</tr>
<tr>
<td><a href="dbxedam.html">dbxedam</a></td>
<td>
Index the EDAM ontology using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxfasta.html">dbxfasta</a></td>
<td>
Index a fasta file database using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxflat.html">dbxflat</a></td>
<td>
Index a flat file database using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxgcg.html">dbxgcg</a></td>
<td>
Index a GCG formatted database using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxobo.html">dbxobo</a></td>
<td>
Index an obo ontology using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxreport.html">dbxreport</a></td>
<td>
Validate index and report internals for dbx databases
</td>
</tr>
<tr>
<td><a href="dbxresource.html">dbxresource</a></td>
<td>
Index a data resource catalogue using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxstat.html">dbxstat</a></td>
<td>
Dump statistics for dbx databases
</td>
</tr>
<tr>
<td><a href="dbxtax.html">dbxtax</a></td>
<td>
Index NCBI taxonomy using b+tree indices
</td>
</tr>
<tr>
<td><a href="dbxuncompress.html">dbxuncompress</a></td>
<td>
Uncompress a compressed dbx index
</td>
</tr>
<tr>
<td><a href="degapseq.html">degapseq</a></td>
<td>
Remove non-alphabetic (e.g. gap) characters from sequences
</td>
</tr>
<tr>
<td><a href="density.html">density</a></td>
<td>
Draw a nucleic acid density plot
</td>
</tr>
<tr>
<td><a href="descseq.html">descseq</a></td>
<td>
Alter the name or description of a sequence
</td>
</tr>
<tr>
<td><a href="diffseq.html">diffseq</a></td>
<td>
Compare and report features of two similar sequences
</td>
</tr>
<tr>
<td><a href="distmat.html">distmat</a></td>
<td>
Create a distance matrix from a multiple sequence alignment
</td>
</tr>
<tr>
<td><a href="dotmatcher.html">dotmatcher</a></td>
<td>
Draw a threshold dotplot of two sequences
</td>
</tr>
<tr>
<td><a href="dotpath.html">dotpath</a></td>
<td>
Draw a non-overlapping wordmatch dotplot of two sequences
</td>
</tr>
<tr>
<td><a href="dottup.html">dottup</a></td>
<td>
Display a wordmatch dotplot of two sequences
</td>
</tr>
<tr>
<td><a href="dreg.html">dreg</a></td>
<td>
Regular expression search of nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="drfinddata.html">drfinddata</a></td>
<td>
Find public databases by data type
</td>
</tr>
<tr>
<td><a href="drfindformat.html">drfindformat</a></td>
<td>
Find public databases by format
</td>
</tr>
<tr>
<td><a href="drfindid.html">drfindid</a></td>
<td>
Find public databases by identifier
</td>
</tr>
<tr>
<td><a href="drfindresource.html">drfindresource</a></td>
<td>
Find public databases by resource
</td>
</tr>
<tr>
<td><a href="drget.html">drget</a></td>
<td>
Get data resource entries
</td>
</tr>
<tr>
<td><a href="drtext.html">drtext</a></td>
<td>
Get data resource entries complete text
</td>
</tr>
<tr>
<td><a href="edamdef.html">edamdef</a></td>
<td>
Find EDAM ontology terms by definition
</td>
</tr>
<tr>
<td><a href="edamhasinput.html">edamhasinput</a></td>
<td>
Find EDAM ontology terms by has_input relation
</td>
</tr>
<tr>
<td><a href="edamhasoutput.html">edamhasoutput</a></td>
<td>
Find EDAM ontology terms by has_output relation
</td>
</tr>
<tr>
<td><a href="edamisformat.html">edamisformat</a></td>
<td>
Find EDAM ontology terms by is_format_of relation
</td>
</tr>
<tr>
<td><a href="edamisid.html">edamisid</a></td>
<td>
Find EDAM ontology terms by is_identifier_of relation
</td>
</tr>
<tr>
<td><a href="edamname.html">edamname</a></td>
<td>
Find EDAM ontology terms by name
</td>
</tr>
<tr>
<td><a href="edialign.html">edialign</a></td>
<td>
Local multiple alignment of sequences
</td>
</tr>
<tr>
<td><a href="einverted.html">einverted</a></td>
<td>
Find inverted repeats in nucleotide sequences
</td>
</tr>
<tr>
<td><a href="embossdata.html">embossdata</a></td>
<td>
Find and retrieve EMBOSS data files
</td>
</tr>
<tr>
<td><a href="embossupdate.html">embossupdate</a></td>
<td>
Check for more recent updates to EMBOSS
</td>
</tr>
<tr>
<td><a href="embossversion.html">embossversion</a></td>
<td>
Report the current EMBOSS version number
</td>
</tr>
<tr>
<td><a href="emma.html">emma</a></td>
<td>
Multiple sequence alignment (ClustalW wrapper)
</td>
</tr>
<tr>
<td><a href="emowse.html">emowse</a></td>
<td>
Search protein sequences by digest fragment molecular weight
</td>
</tr>
<tr>
<td><a href="entret.html">entret</a></td>
<td>
Retrieve sequence entries from flatfile databases and files
</td>
</tr>
<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>
Find PEST motifs as potential proteolytic cleavage sites
</td>
</tr>
<tr>
<td><a href="eprimer3.html">eprimer3</a></td>
<td>
Pick PCR primers and hybridization oligos
</td>
</tr>
<tr>
<td><a href="eprimer32.html">eprimer32</a></td>
<td>
Pick PCR primers and hybridization oligos
</td>
</tr>
<tr>
<td><a href="equicktandem.html">equicktandem</a></td>
<td>
Find tandem repeats in nucleotide sequences
</td>
</tr>
<tr>
<td><a href="est2genome.html">est2genome</a></td>
<td>
Align EST sequences to genomic DNA sequence
</td>
</tr>
<tr>
<td><a href="etandem.html">etandem</a></td>
<td>
Find tandem repeats in a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>
Extract regions from a sequence alignment
</td>
</tr>
<tr>
<td><a href="extractfeat.html">extractfeat</a></td>
<td>
Extract features from sequence(s)
</td>
</tr>
<tr>
<td><a href="extractseq.html">extractseq</a></td>
<td>
Extract regions from a sequence
</td>
</tr>
<tr>
<td><a href="featcopy.html">featcopy</a></td>
<td>
Read and write a feature table
</td>
</tr>
<tr>
<td><a href="featmerge.html">featmerge</a></td>
<td>
Merge two overlapping feature tables
</td>
</tr>
<tr>
<td><a href="featreport.html">featreport</a></td>
<td>
Read and write a feature table
</td>
</tr>
<tr>
<td><a href="feattext.html">feattext</a></td>
<td>
Return a feature table original text
</td>
</tr>
<tr>
<td><a href="findkm.html">findkm</a></td>
<td>
Calculate and plot enzyme reaction data
</td>
</tr>
<tr>
<td><a href="freak.html">freak</a></td>
<td>
Generate residue/base frequency table or plot
</td>
</tr>
<tr>
<td><a href="fuzznuc.html">fuzznuc</a></td>
<td>
Search for patterns in nucleotide sequences
</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>
Search for patterns in protein sequences
</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>
Search for patterns in protein sequences (translated)
</td>
</tr>
<tr>
<td><a href="garnier.html">garnier</a></td>
<td>
Predict protein secondary structure using GOR method
</td>
</tr>
<tr>
<td><a href="geecee.html">geecee</a></td>
<td>
Calculate fractional GC content of nucleic acid sequences
</td>
</tr>
<tr>
<td><a href="getorf.html">getorf</a></td>
<td>
Find and extract open reading frames (ORFs)
</td>
</tr>
<tr>
<td><a href="godef.html">godef</a></td>
<td>
Find GO ontology terms by definition
</td>
</tr>
<tr>
<td><a href="goname.html">goname</a></td>
<td>
Find GO ontology terms by name
</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>
Identify nucleic acid-binding motifs in protein sequences
</td>
</tr>
<tr>
<td><a href="hmoment.html">hmoment</a></td>
<td>
Calculate and plot hydrophobic moment for protein sequence(s)
</td>
</tr>
<tr>
<td><a href="iep.html">iep</a></td>
<td>
Calculate the isoelectric point of proteins
</td>
</tr>
<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>
Display basic information about a multiple sequence alignment
</td>
</tr>
<tr>
<td><a href="infoassembly.html">infoassembly</a></td>
<td>
Display information about assemblies
</td>
</tr>
<tr>
<td><a href="infobase.html">infobase</a></td>
<td>
Return information on a given nucleotide base
</td>
</tr>
<tr>
<td><a href="inforesidue.html">inforesidue</a></td>
<td>
Return information on a given amino acid residue
</td>
</tr>
<tr>
<td><a href="infoseq.html">infoseq</a></td>
<td>
Display basic information about sequences
</td>
</tr>
<tr>
<td><a href="isochore.html">isochore</a></td>
<td>
Plot isochores in DNA sequences
</td>
</tr>
<tr>
<td><a href="jaspextract.html">jaspextract</a></td>
<td>
Extract data from JASPAR
</td>
</tr>
<tr>
<td><a href="jaspscan.html">jaspscan</a></td>
<td>
Scan DNA sequences for transcription factors
</td>
</tr>
<tr>
<td><a href="lindna.html">lindna</a></td>
<td>
Draw linear maps of DNA constructs
</td>
</tr>
<tr>
<td><a href="listor.html">listor</a></td>
<td>
Write a list file of the logical OR of two sets of sequences
</td>
</tr>
<tr>
<td><a href="makenucseq.html">makenucseq</a></td>
<td>
Create random nucleotide sequences
</td>
</tr>
<tr>
<td><a href="makeprotseq.html">makeprotseq</a></td>
<td>
Create random protein sequences
</td>
</tr>
<tr>
<td><a href="marscan.html">marscan</a></td>
<td>
Find matrix/scaffold recognition (MRS) signatures in DNA sequences
</td>
</tr>
<tr>
<td><a href="maskambignuc.html">maskambignuc</a></td>
<td>
Mask all ambiguity characters in nucleotide sequences with N
</td>
</tr>
<tr>
<td><a href="maskambigprot.html">maskambigprot</a></td>
<td>
Mask all ambiguity characters in protein sequences with X
</td>
</tr>
<tr>
<td><a href="maskfeat.html">maskfeat</a></td>
<td>
Write a sequence with masked features
</td>
</tr>
<tr>
<td><a href="maskseq.html">maskseq</a></td>
<td>
Write a sequence with masked regions
</td>
</tr>
<tr>
<td><a href="matcher.html">matcher</a></td>
<td>
Waterman-Eggert local alignment of two sequences
</td>
</tr>
<tr>
<td><a href="megamerger.html">megamerger</a></td>
<td>
Merge two large overlapping DNA sequences
</td>
</tr>
<tr>
<td><a href="merger.html">merger</a></td>
<td>
Merge two overlapping sequences
</td>
</tr>
<tr>
<td><a href="msbar.html">msbar</a></td>
<td>
Mutate a sequence
</td>
</tr>
<tr>
<td><a href="mwcontam.html">mwcontam</a></td>
<td>
Find weights common to multiple molecular weights files
</td>
</tr>
<tr>
<td><a href="mwfilter.html">mwfilter</a></td>
<td>
Filter noisy data from molecular weights file
</td>
</tr>
<tr>
<td><a href="needle.html">needle</a></td>
<td>
Needleman-Wunsch global alignment of two sequences
</td>
</tr>
<tr>
<td><a href="needleall.html">needleall</a></td>
<td>
Many-to-many pairwise alignments of two sequence sets
</td>
</tr>
<tr>
<td><a href="newcpgreport.html">newcpgreport</a></td>
<td>
Identify CpG islands in nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="newcpgseek.html">newcpgseek</a></td>
<td>
Identify and report CpG-rich regions in nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="newseq.html">newseq</a></td>
<td>
Create a sequence file from a typed-in sequence
</td>
</tr>
<tr>
<td><a href="nohtml.html">nohtml</a></td>
<td>
Remove mark-up (e.g. HTML tags) from an ASCII text file
</td>
</tr>
<tr>
<td><a href="noreturn.html">noreturn</a></td>
<td>
Remove carriage return from ASCII files
</td>
</tr>
<tr>
<td><a href="nospace.html">nospace</a></td>
<td>
Remove whitespace from an ASCII text file
</td>
</tr>
<tr>
<td><a href="notab.html">notab</a></td>
<td>
Replace tabs with spaces in an ASCII text file
</td>
</tr>
<tr>
<td><a href="notseq.html">notseq</a></td>
<td>
Write to file a subset of an input stream of sequences
</td>
</tr>
<tr>
<td><a href="nthseq.html">nthseq</a></td>
<td>
Write to file a single sequence from an input stream of sequences
</td>
</tr>
<tr>
<td><a href="nthseqset.html">nthseqset</a></td>
<td>
Read and write (return) one set of sequences from many
</td>
</tr>
<tr>
<td><a href="octanol.html">octanol</a></td>
<td>
Draw a White-Wimley protein hydropathy plot
</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>
Identify proteins with specified sequence word composition
</td>
</tr>
<tr>
<td><a href="ontocount.html">ontocount</a></td>
<td>
Count ontology term(s)
</td>
</tr>
<tr>
<td><a href="ontoget.html">ontoget</a></td>
<td>
Get ontology term(s)
</td>
</tr>
<tr>
<td><a href="ontogetcommon.html">ontogetcommon</a></td>
<td>
Get common ancestor for terms
</td>
</tr>
<tr>
<td><a href="ontogetdown.html">ontogetdown</a></td>
<td>
Get ontology term(s) by parent id
</td>
</tr>
<tr>
<td><a href="ontogetobsolete.html">ontogetobsolete</a></td>
<td>
Get ontology ontology terms
</td>
</tr>
<tr>
<td><a href="ontogetroot.html">ontogetroot</a></td>
<td>
Get ontology root terms by child identifier
</td>
</tr>
<tr>
<td><a href="ontogetsibs.html">ontogetsibs</a></td>
<td>
Get ontology term(s) by id with common parent
</td>
</tr>
<tr>
<td><a href="ontogetup.html">ontogetup</a></td>
<td>
Get ontology term(s) by id of child
</td>
</tr>
<tr>
<td><a href="ontoisobsolete.html">ontoisobsolete</a></td>
<td>
Report whether an ontology term id is obsolete
</td>
</tr>
<tr>
<td><a href="ontotext.html">ontotext</a></td>
<td>
Get ontology term(s) original full text
</td>
</tr>
<tr>
<td><a href="palindrome.html">palindrome</a></td>
<td>
Find inverted repeats in nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="pasteseq.html">pasteseq</a></td>
<td>
Insert one sequence into another
</td>
</tr>
<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>
Search protein sequences with a sequence motif
</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>
Scan a protein sequence with motifs from the PROSITE database
</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>
Predict coiled coil regions in protein sequences
</td>
</tr>
<tr>
<td><a href="pepdigest.html">pepdigest</a></td>
<td>
Report on protein proteolytic enzyme or reagent cleavage sites
</td>
</tr>
<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>
Plot amino acid properties of a protein sequence in parallel
</td>
</tr>
<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>
Draw a helical net for a protein sequence
</td>
</tr>
<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>
Calculate statistics of protein properties
</td>
</tr>
<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>
Draw a helical wheel diagram for a protein sequence
</td>
</tr>
<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>
Draw a hydropathy plot for a protein sequence
</td>
</tr>
<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>
Draw Kyte-Doolittle hydropathy plot for a protein alignment
</td>
</tr>
<tr>
<td><a href="plotcon.html">plotcon</a></td>
<td>
Plot conservation of a sequence alignment
</td>
</tr>
<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>
Plot potential open reading frames in a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="polydot.html">polydot</a></td>
<td>
Draw dotplots for all-against-all comparison of a sequence set
</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>
Regular expression search of protein sequence(s)
</td>
</tr>
<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>
Draw a sequence alignment with pretty formatting
</td>
</tr>
<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>
Write a nucleotide sequence and its translation to file
</td>
</tr>
<tr>
<td><a href="primersearch.html">primersearch</a></td>
<td>
Search DNA sequences for matches with primer pairs
</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>
Extract data from PRINTS database for use by pscan
</td>
</tr>
<tr>
<td><a href="profit.html">profit</a></td>
<td>
Scan one or more sequences with a simple frequency matrix
</td>
</tr>
<tr>
<td><a href="prophecy.html">prophecy</a></td>
<td>
Create frequency matrix or profile from a multiple alignment
</td>
</tr>
<tr>
<td><a href="prophet.html">prophet</a></td>
<td>
Scan one or more sequences with a Gribskov or Henikoff profile
</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>
Process the PROSITE motif database for use by patmatmotifs
</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>
Scan protein sequence(s) with fingerprints from the PRINTS database
</td>
</tr>
<tr>
<td><a href="psiphi.html">psiphi</a></td>
<td>
Calculates phi and psi torsion angles from protein coordinates
</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>
Process the REBASE database for use by restriction enzyme applications
</td>
</tr>
<tr>
<td><a href="recoder.html">recoder</a></td>
<td>
Find restriction sites to remove (mutate) with no translation change
</td>
</tr>
<tr>
<td><a href="redata.html">redata</a></td>
<td>
Retrieve information from REBASE restriction enzyme database
</td>
</tr>
<tr>
<td><a href="refseqget.html">refseqget</a></td>
<td>
Get reference sequence
</td>
</tr>
<tr>
<td><a href="remap.html">remap</a></td>
<td>
Display restriction enzyme binding sites in a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="restover.html">restover</a></td>
<td>
Find restriction enzymes producing a specific overhang
</td>
</tr>
<tr>
<td><a href="restrict.html">restrict</a></td>
<td>
Report restriction enzyme cleavage sites in a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="revseq.html">revseq</a></td>
<td>
Reverse and complement a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="seealso.html">seealso</a></td>
<td>
Find programs with similar function to a specified program
</td>
</tr>
<tr>
<td><a href="seqcount.html">seqcount</a></td>
<td>
Read and count sequences
</td>
</tr>
<tr>
<td><a href="seqmatchall.html">seqmatchall</a></td>
<td>
All-against-all word comparison of a sequence set
</td>
</tr>
<tr>
<td><a href="seqret.html">seqret</a></td>
<td>
Read and write (return) sequences
</td>
</tr>
<tr>
<td><a href="seqretsetall.html">seqretsetall</a></td>
<td>
Read and write (return) many sets of sequences
</td>
</tr>
<tr>
<td><a href="seqretsplit.html">seqretsplit</a></td>
<td>
Read sequences and write them to individual files
</td>
</tr>
<tr>
<td><a href="seqxref.html">seqxref</a></td>
<td>
Retrieve all database cross-references for a sequence entry
</td>
</tr>
<tr>
<td><a href="seqxrefget.html">seqxrefget</a></td>
<td>
Retrieve all cross-referenced data for a sequence entry
</td>
</tr>
<tr>
<td><a href="servertell.html">servertell</a></td>
<td>
Display information about a public server
</td>
</tr>
<tr>
<td><a href="showalign.html">showalign</a></td>
<td>
Display a multiple sequence alignment in pretty format
</td>
</tr>
<tr>
<td><a href="showdb.html">showdb</a></td>
<td>
Display information on configured databases
</td>
</tr>
<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>
Display features of a sequence in pretty format
</td>
</tr>
<tr>
<td><a href="showorf.html">showorf</a></td>
<td>
Display a nucleotide sequence and translation in pretty format
</td>
</tr>
<tr>
<td><a href="showpep.html">showpep</a></td>
<td>
Display protein sequences with features in pretty format
</td>
</tr>
<tr>
<td><a href="showseq.html">showseq</a></td>
<td>
Display sequences with features in pretty format
</td>
</tr>
<tr>
<td><a href="showserver.html">showserver</a></td>
<td>
Display information on configured servers
</td>
</tr>
<tr>
<td><a href="shuffleseq.html">shuffleseq</a></td>
<td>
Shuffle a set of sequences maintaining composition
</td>
</tr>
<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>
Report on signal cleavage sites in a protein sequence
</td>
</tr>
<tr>
<td><a href="silent.html">silent</a></td>
<td>
Find restriction sites to insert (mutate) with no translation change
</td>
</tr>
<tr>
<td><a href="sirna.html">sirna</a></td>
<td>
Find siRNA duplexes in mRNA
</td>
</tr>
<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>
Display a DNA sequence with 6-frame translation and ORFs
</td>
</tr>
<tr>
<td><a href="sizeseq.html">sizeseq</a></td>
<td>
Sort sequences by size
</td>
</tr>
<tr>
<td><a href="skipredundant.html">skipredundant</a></td>
<td>
Remove redundant sequences from an input set
</td>
</tr>
<tr>
<td><a href="skipseq.html">skipseq</a></td>
<td>
Read and write (return) sequences, skipping first few
</td>
</tr>
<tr>
<td><a href="splitsource.html">splitsource</a></td>
<td>
Split sequence(s) into original source sequences
</td>
</tr>
<tr>
<td><a href="splitter.html">splitter</a></td>
<td>
Split sequence(s) into smaller sequences
</td>
</tr>
<tr>
<td><a href="stretcher.html">stretcher</a></td>
<td>
Needleman-Wunsch rapid global alignment of two sequences
</td>
</tr>
<tr>
<td><a href="stssearch.html">stssearch</a></td>
<td>
Search a DNA database for matches with a set of STS primers
</td>
</tr>
<tr>
<td><a href="supermatcher.html">supermatcher</a></td>
<td>
Calculate approximate local pair-wise alignments of larger sequences
</td>
</tr>
<tr>
<td><a href="syco.html">syco</a></td>
<td>
Draw synonymous codon usage statistic plot for a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="taxget.html">taxget</a></td>
<td>
Get taxon(s)
</td>
</tr>
<tr>
<td><a href="taxgetdown.html">taxgetdown</a></td>
<td>
Get descendants of taxon(s)
</td>
</tr>
<tr>
<td><a href="taxgetrank.html">taxgetrank</a></td>
<td>
Get parents of taxon(s)
</td>
</tr>
<tr>
<td><a href="taxgetspecies.html">taxgetspecies</a></td>
<td>
Get all species under taxon(s)
</td>
</tr>
<tr>
<td><a href="taxgetup.html">taxgetup</a></td>
<td>
Get parents of taxon(s)
</td>
</tr>
<tr>
<td><a href="tcode.html">tcode</a></td>
<td>
Identify protein-coding regions using Fickett TESTCODE statistic
</td>
</tr>
<tr>
<td><a href="textget.html">textget</a></td>
<td>
Get text data entries
</td>
</tr>
<tr>
<td><a href="textsearch.html">textsearch</a></td>
<td>
Search the textual description of sequence(s)
</td>
</tr>
<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>
Process TRANSFAC transcription factor database for use by tfscan
</td>
</tr>
<tr>
<td><a href="tfm.html">tfm</a></td>
<td>
Display full documentation for an application
</td>
</tr>
<tr>
<td><a href="tfscan.html">tfscan</a></td>
<td>
Identify transcription factor binding sites in DNA sequences
</td>
</tr>
<tr>
<td><a href="tmap.html">tmap</a></td>
<td>
Predict and plot transmembrane segments in protein sequences
</td>
</tr>
<tr>
<td><a href="tranalign.html">tranalign</a></td>
<td>
Generate an alignment of nucleic coding regions from aligned proteins
</td>
</tr>
<tr>
<td><a href="transeq.html">transeq</a></td>
<td>
Translate nucleic acid sequences
</td>
</tr>
<tr>
<td><a href="trimest.html">trimest</a></td>
<td>
Remove poly-A tails from nucleotide sequences
</td>
</tr>
<tr>
<td><a href="trimseq.html">trimseq</a></td>
<td>
Remove unwanted characters from start and end of sequence(s)
</td>
</tr>
<tr>
<td><a href="trimspace.html">trimspace</a></td>
<td>
Remove extra whitespace from an ASCII text file
</td>
</tr>
<tr>
<td><a href="twofeat.html">twofeat</a></td>
<td>
Find neighbouring pairs of features in sequence(s)
</td>
</tr>
<tr>
<td><a href="union.html">union</a></td>
<td>
Concatenate multiple sequences into a single sequence
</td>
</tr>
<tr>
<td><a href="urlget.html">urlget</a></td>
<td>
Get URLs of data resources
</td>
</tr>
<tr>
<td><a href="variationget.html">variationget</a></td>
<td>
Get sequence variations
</td>
</tr>
<tr>
<td><a href="vectorstrip.html">vectorstrip</a></td>
<td>
Remove vectors from the ends of nucleotide sequence(s)
</td>
</tr>
<tr>
<td><a href="water.html">water</a></td>
<td>
Smith-Waterman local alignment of sequences
</td>
</tr>
<tr>
<td><a href="whichdb.html">whichdb</a></td>
<td>
Search all sequence databases for an entry and retrieve it
</td>
</tr>
<tr>
<td><a href="wobble.html">wobble</a></td>
<td>
Plot third base position variability in a nucleotide sequence
</td>
</tr>
<tr>
<td><a href="wordcount.html">wordcount</a></td>
<td>
Count and extract unique words in molecular sequence(s)
</td>
</tr>
<tr>
<td><a href="wordfinder.html">wordfinder</a></td>
<td>
Match large sequences against one or more other sequences
</td>
</tr>
<tr>
<td><a href="wordmatch.html">wordmatch</a></td>
<td>
Find regions of identity (exact matches) of two sequences
</td>
</tr>
<tr>
<td><a href="wossdata.html">wossdata</a></td>
<td>
Find programs by EDAM data
</td>
</tr>
<tr>
<td><a href="wossinput.html">wossinput</a></td>
<td>
Find programs by EDAM input data
</td>
</tr>
<tr>
<td><a href="wossname.html">wossname</a></td>
<td>
Find programs by keywords in their short description
</td>
</tr>
<tr>
<td><a href="wossoperation.html">wossoperation</a></td>
<td>
Find programs by EDAM operation
</td>
</tr>
<tr>
<td><a href="wossoutput.html">wossoutput</a></td>
<td>
Find programs by EDAM output data
</td>
</tr>
<tr>
<td><a href="wossparam.html">wossparam</a></td>
<td>
Find programs by EDAM parameter
</td>
</tr>
<tr>
<td><a href="wosstopic.html">wosstopic</a></td>
<td>
Find programs by EDAM topic
</td>
</tr>
<tr>
<td><a href="xmlget.html">xmlget</a></td>
<td>
Get XML data
</td>
</tr>
<tr>
<td><a href="xmltext.html">xmltext</a></td>
<td>
Get XML document original full text
</td>
</tr>
<tr>
<td><a href="yank.html">yank</a></td>
<td>
Add a sequence reference (a full USA) to a list file
</td>
</tr>


</table>




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