Changes

From Opengenome.net

Sequence alignment software

37,264 bytes added, 20:57, 8 November 2008
no edit summary
<p><font size="4"><font size="5">Pairwise sequence alignment and multiple sequence alignment software list</font><br />
</font><br />
See structural alignment software for [[Structural alignment of proteins]].</p>
<p>&nbsp;</p>
<h2><span class="mw-headline"><font size="4">Database search only</font></span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Description</th>
<th>Sequence Type*</th>
<th>Link</th>
</tr>
<tr>
<td>FASTA</td>
<td><em>k</em>-tuple local search</td>
<td>Both</td>
<td><a class="external text" title="http://www.ebi.ac.uk/fasta33/index.html" rel="nofollow" href="http://www.ebi.ac.uk/fasta33/index.html">EBI</a> <a class="external text" title="http://fasta.genome.jp/" rel="nofollow" href="http://fasta.genome.jp/">GenomeNet</a> <a class="external text" title="http://pir.georgetown.edu/pirwww/search/fasta.shtml" rel="nofollow" href="http://pir.georgetown.edu/pirwww/search/fasta.shtml">PIR</a> (protein only)</td>
</tr>
<tr>
<td>BLAST</td>
<td><em>k</em>-tuple local search (Basic Local Alignment Search Tool)</td>
<td>Both</td>
<td><a class="external text" title="http://ncbi.nih.gov/BLAST/" rel="nofollow" href="http://ncbi.nih.gov/BLAST/">NCBI</a> <a class="external text" title="http://www.ebi.ac.uk/blast/" rel="nofollow" href="http://www.ebi.ac.uk/blast/">EBI</a> <a class="external text" title="http://blast.genome.jp/" rel="nofollow" href="http://blast.genome.jp/">GenomeNet</a> <a class="external text" title="http://pir.georgetown.edu/pirwww/search/blast.shtml" rel="nofollow" href="http://pir.georgetown.edu/pirwww/search/blast.shtml">PIR</a> (protein only)</td>
</tr>
<tr>
<td>GGSEARCH / GLSEARCH</td>
<td>Global:Global (GG), Global:Local (GL) alignment with statistics</td>
<td>Protein</td>
<td><a class="external text" title="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=select&amp;pgm=gnw" rel="nofollow" href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=select&amp;pgm=gnw">FASTA server</a></td>
</tr>
<tr>
<td>SSEARCH</td>
<td>Smith-Waterman search (more sensitive than FASTA)</td>
<td>Both</td>
<td><a class="external text" title="http://www.ebi.ac.uk/fasta33/index.html" rel="nofollow" href="http://www.ebi.ac.uk/fasta33/index.html">EBI</a> <a class="external text" title="http://ori.nibb.ac.jp/SIT/SSEARCH.html" rel="nofollow" href="http://ori.nibb.ac.jp/SIT/SSEARCH.html">server</a></td>
</tr>
<tr>
<td>HMMer</td>
<td>Hidden Markov profile search</td>
<td>Protein/DNA</td>
<td><a class="external text" title="http://hmmer.janelia.org/" rel="nofollow" href="http://hmmer.janelia.org/">download</a> (S. Eddy)</td>
</tr>
<tr>
<td>SAM</td>
<td>Hidden Markov profile search</td>
<td>Protein/DNA</td>
<td><a class="external text" title="http://www.cse.ucsc.edu/research/compbio/sam.html" rel="nofollow" href="http://www.cse.ucsc.edu/research/compbio/sam.html">SAM</a> (K. Karplus, A. Krogh)</td>
</tr>
<tr>
<td>Combinatorial Extension</td>
<td>Structural alignment search</td>
<td>Protein</td>
<td><a class="external text" title="http://cl.sdsc.edu/" rel="nofollow" href="http://cl.sdsc.edu/">server</a></td>
</tr>
<tr>
<td>IDF</td>
<td>Inverse Document Frequency</td>
<td>Both</td>
<td><a class="external text" title="http://www.cs.uni.edu/~okane/source/IDF/idf.html" rel="nofollow" href="http://www.cs.uni.edu/~okane/source/IDF/idf.html">Download</a></td>
</tr>
<tr>
<td style="BORDER-TOP: #333 1px solid" colspan="4"><small><font size="2">*<strong>Sequence Type:</strong> Protein or nucleotide</font></small></td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<h2><span class="mw-headline"><font size="4">Pairwise alignment</font></span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Description</th>
<th>Sequence Type*</th>
<th>Alignment Type**</th>
<th>Link</th>
<th>Author</th>
<th>Year</th>
</tr>
<tr>
<td>BLASTZ</td>
<td>Seeded pattern-matching</td>
<td>Nucleotide</td>
<td>Local</td>
<td><a class="external text" title="http://www.bx.psu.edu/miller_lab/dist/blastz-2004-12-27.tar.gz" rel="nofollow" href="http://www.bx.psu.edu/miller_lab/dist/blastz-2004-12-27.tar.gz">download</a></td>
<td>Schwartz <em>et al.</em></td>
<td>2003</td>
</tr>
<tr>
<td>DNADot</td>
<td>Web-based dot-plot tool</td>
<td>Nucleotide</td>
<td>Global</td>
<td><a class="external text" title="http://www.vivo.colostate.edu/molkit/dnadot/index.html" rel="nofollow" href="http://www.vivo.colostate.edu/molkit/dnadot/index.html">server</a></td>
<td>R. Bowen</td>
<td>1998</td>
</tr>
<tr>
<td>DOTLET</td>
<td>Java-based dot-plot tool</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html" rel="nofollow" href="http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html">applet</a></td>
<td>M. Pagni and T. Junier</td>
<td>1998</td>
</tr>
<tr>
<td>GGSEARCH, GLSEARCH</td>
<td>Global:Global (GG), Global:Local (GL) alignment with statistics</td>
<td>Protein</td>
<td>Global in query</td>
<td><a class="external text" title="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=compare&amp;pgm=gnw" rel="nofollow" href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=compare&amp;pgm=gnw">FASTA server</a></td>
<td>W. Pearson</td>
<td>2007</td>
</tr>
<tr>
<td>JAligner</td>
<td>Open source Java implementation of Smith-Waterman</td>
<td>Both</td>
<td>Local</td>
<td><a class="external text" title="http://jaligner.sourceforge.net" rel="nofollow" href="http://jaligner.sourceforge.net/">JWS</a></td>
<td>A. Moustafa</td>
<td>2005</td>
</tr>
<tr>
<td>LALIGN</td>
<td>Multiple, non-overlapping, local similarity (same algorithm as SIM)</td>
<td>Both</td>
<td>Local non-overlapping</td>
<td><a class="external text" title="http://www.ch.embnet.org/software/LALIGN_form.html" rel="nofollow" href="http://www.ch.embnet.org/software/LALIGN_form.html">server</a> <a class="external text" title="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=lalign" rel="nofollow" href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=lalign">FASTA server</a></td>
<td>W. Pearson</td>
<td>1991 (algorithm)</td>
</tr>
<tr>
<td>matcher</td>
<td>Memory-optimized needleman but slow dynamic programming (based on LALIGN)</td>
<td>Both</td>
<td>Local</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/matcher.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/matcher.html">server</a></td>
<td>I. Longden (modified from W. Pearson)</td>
<td>1999</td>
</tr>
<tr>
<td>MCALIGN2</td>
<td>explicit models of indel evolution</td>
<td>DNA</td>
<td>Global</td>
<td><a class="external text" title="http://homepages.ed.ac.uk/eang33/mcalign/mcinstructions.html" rel="nofollow" href="http://homepages.ed.ac.uk/eang33/mcalign/mcinstructions.html">server</a></td>
<td>J. Wang <em>et al.</em></td>
<td>2006</td>
</tr>
<tr>
<td>MUMmer</td>
<td>Suffix-Tree based</td>
<td>Nucleotide</td>
<td>Global</td>
<td><a class="external text" title="http://mummer.sourceforge.net/" rel="nofollow" href="http://mummer.sourceforge.net/">download</a></td>
<td>S. Kurtz <em>et al.</em></td>
<td>2004</td>
</tr>
<tr>
<td>needle</td>
<td>Needleman-Wunsch dynamic programming</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/needle.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/needle.html">server</a></td>
<td>A. Bleasby</td>
<td>1999</td>
</tr>
<tr>
<td>Ngila</td>
<td>logarithmic and affine gap costs and explicit models of indel evolution</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://scit.us/projects/ngila/" rel="nofollow" href="http://scit.us/projects/ngila/">download</a></td>
<td>R. Cartwright</td>
<td>2007</td>
</tr>
<tr>
<td>PatternHunter</td>
<td>Seeded pattern-matching</td>
<td>Nucleotide</td>
<td>Local</td>
<td><a class="external text" title="http://www.bioinformaticssolutions.com/products/ph/download_academ.php" rel="nofollow" href="http://www.bioinformaticssolutions.com/products/ph/download_academ.php">download</a></td>
<td>B. Ma <em>et al.</em></td>
<td>2002-2004</td>
</tr>
<tr>
<td>ProbA (also propA)</td>
<td>Stochastic partition function sampling via dynamic programming</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://www.tbi.univie.ac.at/%7Eulim/probA/index.html" rel="nofollow" href="http://www.tbi.univie.ac.at/~ulim/probA/index.html">download</a></td>
<td>U. M&uuml;ckstein</td>
<td>2002</td>
</tr>
<tr>
<td>PyMOL</td>
<td>&quot;align&quot; command aligns sequence &amp; applies it to structure</td>
<td>Protein</td>
<td>Global (by selection)</td>
<td><a class="external text" title="http://pymol.sf.net" rel="nofollow" href="http://pymol.sf.net/">site</a></td>
<td>W. L. DeLano</td>
<td>2007</td>
</tr>
<tr>
<td>REPuter</td>
<td>Suffix-Tree based</td>
<td>Nucleotide</td>
<td>Local</td>
<td><a class="external text" title="http://bibiserv.techfak.uni-bielefeld.de/reputer/" rel="nofollow" href="http://bibiserv.techfak.uni-bielefeld.de/reputer/">download</a></td>
<td>S. Kurtz <em>et al.</em></td>
<td>2001</td>
</tr>
<tr>
<td>SEQALN</td>
<td>Various dynamic programming</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www-hto.usc.edu/software/seqaln/seqaln-query.html" rel="nofollow" href="http://www-hto.usc.edu/software/seqaln/seqaln-query.html">server</a></td>
<td>M.S. Waterman and P. Hardy</td>
<td>1996</td>
</tr>
<tr>
<td>SIM, GAP, NAP, LAP</td>
<td>Local similarity with varying gap treatments</td>
<td>Both</td>
<td>Local or global</td>
<td><a class="external text" title="http://genome.cs.mtu.edu/align/align.html" rel="nofollow" href="http://genome.cs.mtu.edu/align/align.html">server</a></td>
<td>X. Huang and W. Miller</td>
<td>1990-6</td>
</tr>
<tr>
<td>SIM</td>
<td>Local similarity</td>
<td>Both</td>
<td>Local</td>
<td><a class="external text" title="http://www.expasy.org/tools/sim.html" rel="nofollow" href="http://www.expasy.org/tools/sim.html">servers</a></td>
<td>X. Huang and W. Miller</td>
<td>1991</td>
</tr>
<tr>
<td>SLIM Search</td>
<td>Ultra-fast blocked alignment</td>
<td>Both</td>
<td>Both</td>
<td><a class="external text" title="http://www.slimsearch.com" rel="nofollow" href="http://www.slimsearch.com/">site</a></td>
<td>L. Bloksberg</td>
<td>2004</td>
</tr>
<tr>
<td>SSEARCH</td>
<td>Local (Smith-Waterman) alignment with statistics</td>
<td>Protein</td>
<td>Local</td>
<td><a class="external text" title="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=compare&amp;pgm=sw" rel="nofollow" href="http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=compare&amp;pgm=sw">FASTA server</a></td>
<td>W. Pearson</td>
<td>1981 (Algorithm)</td>
</tr>
<tr>
<td>stretcher</td>
<td>Memory-optimized but slow dynamic programming</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/matcher.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/matcher.html">server</a></td>
<td>I. Longden (modified from G. Myers and W. Miller)</td>
<td>1999</td>
</tr>
<tr>
<td>tranalign</td>
<td>Aligns nucleic acid sequences given a protein alignment</td>
<td>Nucleotide</td>
<td>NA</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/tranalign.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/tranalign.html">server</a></td>
<td>G. Williams (modified from B. Pearson)</td>
<td>2002</td>
</tr>
<tr>
<td>water</td>
<td>Smith-Waterman dynamic programming</td>
<td>Both</td>
<td>Local</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/water.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/water.html">server</a></td>
<td>A. Bleasby</td>
<td>1999</td>
</tr>
<tr>
<td>wordmatch</td>
<td><em>k</em>-tuple pairwise match</td>
<td>Both</td>
<td>NA</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/wordmatch.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/wordmatch.html">server</a></td>
<td>I. Longden</td>
<td>1998</td>
</tr>
<tr>
<td>YASS</td>
<td>Seeded pattern-matching</td>
<td>Nucleotide</td>
<td>Local</td>
<td><a class="external text" title="http://bioinfo.lifl.fr/yass/yass.php" rel="nofollow" href="http://bioinfo.lifl.fr/yass/yass.php">server</a> <a class="external text" title="http://bioinfo.lifl.fr/yass/download.php" rel="nofollow" href="http://bioinfo.lifl.fr/yass/download.php">download</a></td>
<td>L. Noe and G. Kucherov</td>
<td>2003-2006</td>
</tr>
<tr>
<td>BioPerl dpAlign</td>
<td>dynamic programming</td>
<td>Both</td>
<td>Both + Ends-free</td>
<td><a class="external text" title="http://www.bioperl.org" rel="nofollow" href="http://www.bioperl.org/">site</a></td>
<td>Y. M. Chan</td>
<td>2003</td>
</tr>
<tr>
<td style="BORDER-TOP: #333 1px solid" colspan="7"><small><font size="2">*<strong>Sequence Type:</strong> Protein or nucleotide. **<strong>Alignment Type:</strong> Local or global</font></small></td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<h2><span class="mw-headline">Multiple sequence alignment</span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Description</th>
<th>Sequence Type*</th>
<th>Alignment Type**</th>
<th>Link</th>
<th>Author</th>
<th>Year</th>
</tr>
<tr>
<td>ABA</td>
<td>A-Bruijn alignment</td>
<td>Protein</td>
<td>Global</td>
<td><a class="external text" title="http://nbcr.sdsc.edu/euler/aba_v1.0/" rel="nofollow" href="http://nbcr.sdsc.edu/euler/aba_v1.0/">download</a></td>
<td>B.Raphael<em>et al.</em></td>
<td>2004</td>
</tr>
<tr>
<td>ALE</td>
<td>manual alignment&nbsp;; some software assistance</td>
<td>Nucleotides</td>
<td>Local</td>
<td><a class="external text" title="http://www.red-bean.com/ale/" rel="nofollow" href="http://www.red-bean.com/ale/">download</a></td>
<td>J. Blandy and K. Fogel</td>
<td>1994 (latest version 2007)</td>
</tr>
<tr>
<td>AMAP</td>
<td>Sequence annealing</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://baboon.math.berkeley.edu/mavid/" rel="nofollow" href="http://baboon.math.berkeley.edu/mavid/">server</a></td>
<td>A. Schwartz and L. Pachter</td>
<td>2006</td>
</tr>
<tr>
<td>BAli-Phy</td>
<td>Tree+Multi alignment&nbsp;; Probabilistic/Bayesian&nbsp;; Joint Estimation</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://www.biomath.ucla.edu/msuchard/bali-phy/" rel="nofollow" href="http://www.biomath.ucla.edu/msuchard/bali-phy/">WWW+download</a></td>
<td>BD Redelings and MA Suchard</td>
<td>2005 (latest version 2007)</td>
</tr>
<tr>
<td>CodonCode Aligner</td>
<td>Multi alignment; ClustalW &amp; Phrap support</td>
<td>Nucleotides</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.codoncode.com/aligner/" rel="nofollow" href="http://www.codoncode.com/aligner/">download</a></td>
<td>P. Richterich <em>et al.</em></td>
<td>2003 (latest version 2007)</td>
</tr>
<tr>
<td>ClustalW</td>
<td>Progressive alignment</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.ebi.ac.uk/clustalw/" rel="nofollow" href="http://www.ebi.ac.uk/clustalw/">EBI</a> <a class="external text" title="http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html" rel="nofollow" href="http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html">PBIL</a> <a class="external text" title="http://www.ch.embnet.org/software/ClustalW.html" rel="nofollow" href="http://www.ch.embnet.org/software/ClustalW.html">EMBNet</a> <a class="external text" title="http://align.genome.jp/" rel="nofollow" href="http://align.genome.jp/">GenomeNet</a></td>
<td>Thompson <em>et al.</em></td>
<td>1994</td>
</tr>
<tr>
<td>DNA Baser</td>
<td>Multi alignment</td>
<td>Both</td>
<td>Local or Global + Post processing</td>
<td><a class="external text" title="http://www.dnabaser.com/index.html" rel="nofollow" href="http://www.dnabaser.com/index.html">DNA Baser (commercial)</a></td>
<td>M. Gabriel</td>
<td>released 2005</td>
</tr>
<tr>
<td>Ed'Nimbus</td>
<td>Seeded filtration</td>
<td>Nucleotides</td>
<td>Local</td>
<td><a class="external text" title="http://igm.univ-mlv.fr/~peterlon/officiel/ednimbus/index.php" rel="nofollow" href="http://igm.univ-mlv.fr/~peterlon/officiel/ednimbus/index.php">server</a></td>
<td>P. Peterlongo <em>et al.</em></td>
<td>2006</td>
</tr>
<tr>
<td>Geneious</td>
<td>Progressive/Iterative alignment; ClustalW plugin</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.geneious.com" rel="nofollow" href="http://www.geneious.com/">download</a></td>
<td>A.J. Drummond <em>et al.</em></td>
<td>2005 / 2006</td>
</tr>
<tr>
<td>CHAOS/DIALIGN</td>
<td>Iterative alignment</td>
<td>Both</td>
<td>Local (preferred)</td>
<td><a class="external text" title="http://dialign.gobics.de/chaos-dialign-submission" rel="nofollow" href="http://dialign.gobics.de/chaos-dialign-submission">server</a></td>
<td>M. Brudno and B. Morgenstern</td>
<td>2003</td>
</tr>
<tr>
<td>Kalign</td>
<td>Progressive alignment</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://msa.cgb.ki.se/" rel="nofollow" href="http://msa.cgb.ki.se/">server</a><a class="external text" title="http://www.ebi.ac.uk/kalign/" rel="nofollow" href="http://www.ebi.ac.uk/kalign/">EBI</a> <a class="external text" title="http://toolkit.tuebingen.mpg.de/kalign" rel="nofollow" href="http://toolkit.tuebingen.mpg.de/kalign">MPItoolkit</a></td>
<td>T. Lassmann</td>
<td>2005</td>
</tr>
<tr>
<td>PRRN/PRRP</td>
<td>Iterative alignment (especially refinement)</td>
<td>Protein</td>
<td>Local or Global</td>
<td><a class="external text" title="http://prrn.hgc.jp/" rel="nofollow" href="http://prrn.hgc.jp/">PRRP</a> <a class="external text" title="http://align.genome.jp/prrn/" rel="nofollow" href="http://align.genome.jp/prrn/">PRRN</a></td>
<td>Y. Totoki (based on O. Gotoh)</td>
<td>1991 and later</td>
</tr>
<tr>
<td>POA</td>
<td>Partial order/hidden Markov model</td>
<td>Protein</td>
<td>Local or Global</td>
<td><a class="external text" title="http://sourceforge.net/project/showfiles.php?group_id=168080" rel="nofollow" href="http://sourceforge.net/project/showfiles.php?group_id=168080">download</a></td>
<td>C. Lee</td>
<td>2002</td>
</tr>
<tr>
<td>MSA</td>
<td>Dynamic programming</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html">download</a></td>
<td>D.J. Lipman <em>et al.</em></td>
<td>1989 (modified 1995)</td>
</tr>
<tr>
<td>SAM</td>
<td>Hidden Markov model</td>
<td>Protein</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.cse.ucsc.edu/compbio/HMM-apps/T02-query.html" rel="nofollow" href="http://www.cse.ucsc.edu/compbio/HMM-apps/T02-query.html">server</a></td>
<td>A. Krogh <em>et al.</em></td>
<td>1994 (most recent version 2002)</td>
</tr>
<tr>
<td>ProbCons</td>
<td>Probabilistic/consistency</td>
<td>Protein</td>
<td>Local or Global</td>
<td><a class="external text" title="http://probcons.stanford.edu/index.html" rel="nofollow" href="http://probcons.stanford.edu/index.html">server</a></td>
<td>C. Do <em>et al.</em></td>
<td>2005</td>
</tr>
<tr>
<td>MULTALIN</td>
<td>Dynamic programming/clustering</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://prodes.toulouse.inra.fr/multalin/multalin.html" rel="nofollow" href="http://prodes.toulouse.inra.fr/multalin/multalin.html">server</a></td>
<td>F. Corpet</td>
<td>1988</td>
</tr>
<tr>
<td>MAVID</td>
<td>Progressive alignment</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://baboon.math.berkeley.edu/mavid/" rel="nofollow" href="http://baboon.math.berkeley.edu/mavid/">server</a></td>
<td>N. Bray and L. Pachter</td>
<td>2004</td>
</tr>
<tr>
<td>Multi-LAGAN</td>
<td>Progressive dynamic programming alignment</td>
<td>Both</td>
<td>Global</td>
<td><a class="external text" title="http://genome.lbl.gov/vista/lagan/submit.shtml" rel="nofollow" href="http://genome.lbl.gov/vista/lagan/submit.shtml">server</a></td>
<td>M. Brudno <em>et al.</em></td>
<td>2003</td>
</tr>
<tr>
<td>MUSCLE</td>
<td>Progressive/iterative alignment</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.drive5.com/muscle" rel="nofollow" href="http://www.drive5.com/muscle">server</a></td>
<td>R. Edgar</td>
<td>2004</td>
</tr>
<tr>
<td>MAFFT</td>
<td>Progressive/iterative alignment</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://align.genome.jp/mafft/" rel="nofollow" href="http://align.genome.jp/mafft/">GenomeNet</a> <a class="external text" title="http://timpani.genome.ad.jp/%7Emafft/server/" rel="nofollow" href="http://timpani.genome.ad.jp/~mafft/server/">MAFFT</a></td>
<td>K. Katoh <em>et al.</em></td>
<td>2005</td>
</tr>
<tr>
<td>PSAlign</td>
<td>Alignment preserving non-heuristic</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://faculty.cs.tamu.edu/shsze/psalign/" rel="nofollow" href="http://faculty.cs.tamu.edu/shsze/psalign/">download</a></td>
<td>S.H. Sze, Y. Lu, Q. Yang.</td>
<td>2006</td>
</tr>
<tr>
<td>SAGA</td>
<td>Sequence alignment by genetic algorithm</td>
<td>Protein</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.tcoffee.org/Projects_home_page/saga_home_page.html" rel="nofollow" href="http://www.tcoffee.org/Projects_home_page/saga_home_page.html">download</a></td>
<td>C. Notredame <em>et al.</em></td>
<td>1996 (new version 1998)</td>
</tr>
<tr>
<td>T-Coffee</td>
<td>More sensitive progressive alignment</td>
<td>Both</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.tcoffee.org" rel="nofollow" href="http://www.tcoffee.org/">server</a></td>
<td>C. Notredame <em>et al.</em></td>
<td>2000</td>
</tr>
<tr>
<td>RevTrans</td>
<td>Combines DNA and Protein alignment, by back translating the protein alignment to DNA.</td>
<td>DNA/Protein (special)</td>
<td>Local or Global</td>
<td><a class="external text" title="http://www.cbs.dtu.dk/services/RevTrans/" rel="nofollow" href="http://www.cbs.dtu.dk/services/RevTrans/">server</a></td>
<td>Wernersson and Pedersen</td>
<td>2003 (newest version 2005)</td>
</tr>
<tr>
<td colspan="7"><small><font size="2">*<strong>Sequence Type:</strong> Protein or nucleotide. **<strong>Alignment Type:</strong> Local or global</font></small></td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<h2><span class="mw-headline">Genomics analysis</span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Description</th>
<th>Sequence Type*</th>
<th>Link</th>
</tr>
<tr>
<td>SLAM</td>
<td>Gene finding, alignment, annotation (human-mouse homology identification)</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://baboon.math.berkeley.edu/~syntenic/slam.html" rel="nofollow" href="http://baboon.math.berkeley.edu/~syntenic/slam.html">server</a></td>
</tr>
<tr>
<td>Mauve</td>
<td>Multiple alignment of rearranged genomes</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://gel.ahabs.wisc.edu/mauve/" rel="nofollow" href="http://gel.ahabs.wisc.edu/mauve/">download</a></td>
</tr>
<tr>
<td>MGA</td>
<td>Multiple Genome Aligner</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://bibiserv.techfak.uni-bielefeld.de/mga/" rel="nofollow" href="http://bibiserv.techfak.uni-bielefeld.de/mga/">download</a></td>
</tr>
<tr>
<td>Mulan</td>
<td>Local multiple alignments of genome-length sequences</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://mulan.dcode.org/" rel="nofollow" href="http://mulan.dcode.org/">server</a></td>
</tr>
<tr>
<td>Sequerome</td>
<td>Profiling sequence alignment data with major servers/services</td>
<td>Nucleotide/peptide</td>
<td><a class="external autonumber" title="http://en.wikipedia.org/wiki/Sequerome" rel="nofollow" href="http://en.wikipedia.org/wiki/Sequerome">[1]</a></td>
</tr>
<tr>
<td>AVID</td>
<td>Pairwise global alignment with whole genomes</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://pipeline.lbl.gov/cgi-bin/GenomeVista" rel="nofollow" href="http://pipeline.lbl.gov/cgi-bin/GenomeVista">server</a></td>
</tr>
<tr>
<td>SIBsim4 / Sim4</td>
<td>A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://sibsim4.sourceforge.net/" rel="nofollow" href="http://sibsim4.sourceforge.net/">download</a></td>
</tr>
<tr>
<td>Shuffle-LAGAN</td>
<td>Pairwise glocal alignment of completed genome regions</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://genome.lbl.gov/cgi-bin/VistaInput?align_pgm=slagan&amp;num_seqs=2" rel="nofollow" href="http://genome.lbl.gov/cgi-bin/VistaInput?align_pgm=slagan&amp;num_seqs=2">server</a></td>
</tr>
<tr>
<td>ACT (Artemis Comparison Tool)</td>
<td>Synteny and comparative genomics</td>
<td>Nucleotide</td>
<td><a class="external text" title="http://www.sanger.ac.uk/Software/ACT/" rel="nofollow" href="http://www.sanger.ac.uk/Software/ACT/">server</a></td>
</tr>
<tr>
<td style="BORDER-TOP: #333 1px solid" colspan="4"><small><font size="2">*<strong>Sequence Type:</strong> Protein or nucleotide</font></small></td>
</tr>
</tbody>
</table>
<p><font size="2"><br />
<br clear="all" />
</font></p>
<p>&nbsp;</p>
<h2><span class="mw-headline">Motif finding</span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Description</th>
<th>Sequence Type*</th>
<th>Link</th>
</tr>
<tr>
<td>MEME/MAST</td>
<td>Motif discovery and search</td>
<td>Both</td>
<td><a class="external text" title="http://meme.sdsc.edu/meme/intro.html" rel="nofollow" href="http://meme.sdsc.edu/meme/intro.html">server</a></td>
</tr>
<tr>
<td>BLOCKS</td>
<td>Ungapped motif identification from BLOCKS database</td>
<td>Both</td>
<td><a class="external text" title="http://blocks.fhcrc.org/blocks/blocks_search.html" rel="nofollow" href="http://blocks.fhcrc.org/blocks/blocks_search.html">server</a></td>
</tr>
<tr>
<td>eMOTIF</td>
<td>Extraction and identification of shorter motifs</td>
<td>Both</td>
<td><a class="external text" title="http://motif.stanford.edu/emotif/" rel="nofollow" href="http://motif.stanford.edu/emotif/">servers</a></td>
</tr>
<tr>
<td>Gibbs motif sampler</td>
<td>Stochastic motif extraction by statistical likelihood</td>
<td>Both</td>
<td><a class="external text" title="http://bayesweb.wadsworth.org/gibbs/gibbs.html" rel="nofollow" href="http://bayesweb.wadsworth.org/gibbs/gibbs.html">server</a> (one of many implementations)</td>
</tr>
<tr>
<td>TEIRESIAS</td>
<td>Motif extraction and database search</td>
<td>Both</td>
<td><a class="external text" title="http://web.csb.ias.edu/Tspd.html" rel="nofollow" href="http://web.csb.ias.edu/Tspd.html">server</a></td>
</tr>
<tr>
<td>PRATT</td>
<td>Pattern generation for use with ScanProsite</td>
<td>Protein</td>
<td><a class="external text" title="http://www.expasy.org/tools/pratt/" rel="nofollow" href="http://www.expasy.org/tools/pratt/">server</a></td>
</tr>
<tr>
<td>ScanProsite</td>
<td>Motif database search tool</td>
<td>Protein</td>
<td><a class="external text" title="http://www.expasy.org/tools/scanprosite/" rel="nofollow" href="http://www.expasy.org/tools/scanprosite/">server</a></td>
</tr>
<tr>
<td>PHI-Blast</td>
<td>Motif search and alignment tool</td>
<td>Both</td>
<td><a class="external text" title="http://bioweb.pasteur.fr/seqanal/interfaces/phiblast.html" rel="nofollow" href="http://bioweb.pasteur.fr/seqanal/interfaces/phiblast.html">server</a></td>
</tr>
<tr>
<td>I-sites</td>
<td>Local structure motif library</td>
<td>Protein</td>
<td><a class="external text" title="http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php" rel="nofollow" href="http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php">server</a></td>
</tr>
<tr>
<td colspan="4"><small><font size="2">*<strong>Sequence Type:</strong> Protein or nucleotide</font></small></td>
</tr>
</tbody>
</table>
<p><font size="2"><br />
<br clear="all" />
</font></p>
<p>&nbsp;</p>
<h2><span class="mw-headline">Benchmarking</span></h2>
<table class="wikitable">
<tbody>
<tr>
<th>Name</th>
<th>Link</th>
<th>Authors</th>
</tr>
<tr>
<td>BAliBASE</td>
<td><a class="external text" title="http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE/" rel="nofollow" href="http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE/">download</a></td>
<td>Thompson, Plewniak, Poch</td>
</tr>
<tr>
<td>Prefab</td>
<td><a class="external text" title="http://www.drive5.com/muscle/prefab.htm" rel="nofollow" href="http://www.drive5.com/muscle/prefab.htm">download</a></td>
<td>Edgar</td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
<h2><span class="mw-headline">Viewers</span></h2>
<p>Jalview is a Java multiple sequence alignment viewer, which is used to integrate the results of a secondary structure prediction via the <a class="new" title="JPred" href="http://en.wikipedia.org/w/index.php?title=JPred&amp;action=edit">JPred</a> web server with a multiple sequence alignment given as input or derived during the run of the algorithm.</p>
<p>&nbsp;</p>
<h2><span class="mw-headline">External links</span></h2>
<ul>
<li><a class="external text" title="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=14736341" rel="nofollow" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=14736341">Pollard et al. (2004)</a> <em>(<a title="PubMed Central" href="http://en.wikipedia.org/wiki/PubMed_Central">PubMed Central</a> free fulltext)</em>: The authors discuss LAGAN, CHAOS, and Dialign as the most effective tools tested for certain uses. </li>
</ul>
Retrieved from "http://Opengenome.net/Special:MobileDiff/29210"

Navigation menu