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<HTML>
<HEAD>
<TITLE>
EMBOSS
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
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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>
</td>
<td align=left valign=middle>
<b><font size="+6">
HMM
</font></b>
</td></tr>
</table>
<br>
<p>
<!--END OF HEADER-->
Hidden markov model analysis
<p>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="../embassy/hmmer/ohmmalign.html">ohmmalign</a></td>
<td>
Align sequences with an HMM
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmbuild.html">ohmmbuild</a></td>
<td>
Build HMM
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmcalibrate.html">ohmmcalibrate</a></td>
<td>
Calibrate a hidden Markov model
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmconvert.html">ohmmconvert</a></td>
<td>
Convert between HMM formats
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmemit.html">ohmmemit</a></td>
<td>
Extract HMM sequences
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmfetch.html">ohmmfetch</a></td>
<td>
Extract HMM from a database
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmindex.html">ohmmindex</a></td>
<td>
Index an HMM database
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmpfam.html">ohmmpfam</a></td>
<td>
Align single sequence with an HMM
</td>
</tr>
<tr>
<td><a href="../embassy/hmmer/ohmmsearch.html">ohmmsearch</a></td>
<td>
Search sequence database with an HMM
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmalign.html">ehmmalign</a></td>
<td>
Align sequences to an HMM profile
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmbuild.html">ehmmbuild</a></td>
<td>
Build a profile HMM from an alignment
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmcalibrate.html">ehmmcalibrate</a></td>
<td>
Calibrate HMM search statistics
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmconvert.html">ehmmconvert</a></td>
<td>
Convert between profile HMM file formats
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmemit.html">ehmmemit</a></td>
<td>
Generate sequences from a profile HMM
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmfetch.html">ehmmfetch</a></td>
<td>
Retrieve an HMM from an HMM database
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmindex.html">ehmmindex</a></td>
<td>
Create a binary SSI index for an HMM database
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmpfam.html">ehmmpfam</a></td>
<td>
Search one or more sequences against an HMM database
</td>
</tr>
<tr>
<td><a href="../embassy/hmmernew/ehmmsearch.html">ehmmsearch</a></td>
<td>
Search a sequence database with a profile HMM
</td>
</tr>
<tr>
<td><a href="../embassy/signature/libgen.html">libgen</a></td>
<td>
Generate discriminating elements from alignments
</td>
</tr>
</table>
</BODY>
</HTML>
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