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<HTML>
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<TITLE>
EMBOSS
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<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
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<b><font size="+6">
ALIGNMENT LOCAL
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<p>
<!--END OF HEADER-->
Local sequence alignment
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<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="matcher.html">matcher</a></td>
<td>
Waterman-Eggert local alignment of two sequences
</td>
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<tr>
<td><a href="seqmatchall.html">seqmatchall</a></td>
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All-against-all word comparison of a sequence set
</td>
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<td><a href="supermatcher.html">supermatcher</a></td>
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Calculate approximate local pair-wise alignments of larger sequences
</td>
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<td><a href="water.html">water</a></td>
<td>
Smith-Waterman local alignment of sequences
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<td><a href="wordfinder.html">wordfinder</a></td>
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Match large sequences against one or more other sequences
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<td><a href="wordmatch.html">wordmatch</a></td>
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Find regions of identity (exact matches) of two sequences
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<td><a href="../embassy/domalign/domainalign.html">domainalign</a></td>
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Generate alignments (DAF file) for nodes in a DCF file
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<td><a href="../embassy/domalign/domainrep.html">domainrep</a></td>
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Reorder DCF file to identify representative structures
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<td><a href="../embassy/domalign/seqalign.html">seqalign</a></td>
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Extend alignments (DAF file) with sequences (DHF file)
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<td><a href="../embassy/hmmer/oalistat.html">oalistat</a></td>
<td>
Statistics for multiple alignment files
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