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<HTML>
<HEAD>
<TITLE>
EMBOSS
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<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>
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<td align=left valign=middle>
<b><font size="+6">
NUCLEIC RNA FOLDING
</font></b>
</td></tr>
</table>
<br>
<p>
<!--END OF HEADER-->
RNA folding methods and analysis
<p>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="../embassy/vienna/ovrnaalifold.html">ovrnaalifold</a></td>
<td>
Calculate secondary structures for a set of aligned RNAs
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaalifoldpf.html">ovrnaalifoldpf</a></td>
<td>
Calculate secondary structures for a set of aligned RNAs (partition)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnacofold.html">ovrnacofold</a></td>
<td>
Calculate secondary structures of RNA dimers
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnacofoldconc.html">ovrnacofoldconc</a></td>
<td>
Calculate secondary structures of RNA dimers (concentrations)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnacofoldpf.html">ovrnacofoldpf</a></td>
<td>
Calculate secondary structures of RNA dimers (partitioning)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnadistance.html">ovrnadistance</a></td>
<td>
Calculate distances between RNA secondary structures
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaduplex.html">ovrnaduplex</a></td>
<td>
Predict RNA duplex (hybridization) sites and structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaeval.html">ovrnaeval</a></td>
<td>
Calculate energy of RNA sequences with a given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaevalpair.html">ovrnaevalpair</a></td>
<td>
Calculate energy of RNA sequences on given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnafold.html">ovrnafold</a></td>
<td>
Calculate min. energy RNA structure / pair probabilities (partition)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnafoldpf.html">ovrnafoldpf</a></td>
<td>
Calculate min. energy RNA structure / pair probabilities
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaheat.html">ovrnaheat</a></td>
<td>
Calculate specific heat of RNA melting
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnainverse.html">ovrnainverse</a></td>
<td>
Find RNA sequences with a given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnalfold.html">ovrnalfold</a></td>
<td>
Calculate locally stable secondary structures of RNAs
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnaplot.html">ovrnaplot</a></td>
<td>
Draw RNA secondary structures
</td>
</tr>
<tr>
<td><a href="../embassy/vienna/ovrnasubopt.html">ovrnasubopt</a></td>
<td>
Calculate suboptimal secondary structure of RNA
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrna2dfold.html">vrna2dfold</a></td>
<td>
Calculate RNA structures and samples of k,l neighbourhoods
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaaliduplex.html">vrnaaliduplex</a></td>
<td>
RNA duplex calculation for two sequence alignments
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaalifold.html">vrnaalifold</a></td>
<td>
Calculate secondary structures for a set of aligned RNAs
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaalifoldpf.html">vrnaalifoldpf</a></td>
<td>
Calculate secondary structures for a set of aligned RNAs (partition)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnacofold.html">vrnacofold</a></td>
<td>
Calculate secondary structures of RNA dimers
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnacofoldconc.html">vrnacofoldconc</a></td>
<td>
Calculate secondary structures of RNA dimers (concentrations)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnacofoldpf.html">vrnacofoldpf</a></td>
<td>
Calculate secondary structures of RNA dimers (partitioning)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnadistance.html">vrnadistance</a></td>
<td>
Calculate distances between RNA secondary structures
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaduplex.html">vrnaduplex</a></td>
<td>
Predict RNA duplex (hybridization) sites and structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaeval.html">vrnaeval</a></td>
<td>
Calculate energy of RNA sequences with a given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaevalpair.html">vrnaevalpair</a></td>
<td>
Calculate energy of RNA sequences on given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnafold.html">vrnafold</a></td>
<td>
Calculate min. energy RNA secondary structures and pair probabilities
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnafoldpf.html">vrnafoldpf</a></td>
<td>
Calculate min. energy RNA structures / pair probabilities (partition)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaheat.html">vrnaheat</a></td>
<td>
Calculate specific heat of RNA melting
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnainverse.html">vrnainverse</a></td>
<td>
Find RNA sequences with a given secondary structure
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnalalifoldpf.html">vrnalalifoldpf</a></td>
<td>
Calculate secondary structures for a set of aligned RNAs (partition)
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnalfold.html">vrnalfold</a></td>
<td>
Calculate locally stable secondary structures of RNAs
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnalfoldz.html">vrnalfoldz</a></td>
<td>
Calculate locally stable secondary structures of RNAs plus zscore
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnapkplex.html">vrnapkplex</a></td>
<td>
Calculate RNA structures plus pseudoknots
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaplfold.html">vrnaplfold</a></td>
<td>
Compute avg. pair probabilities for local base pairs in RNA sequences
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnaplot.html">vrnaplot</a></td>
<td>
Draw RNA secondary structures
</td>
</tr>
<tr>
<td><a href="../embassy/vienna2/vrnasubopt.html">vrnasubopt</a></td>
<td>
Calculate suboptimal secondary structures of RNAs
</td>
</tr>
</table>
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