ToolsRNAStructureMutualInformation < Lab

<table><tr><td width=88><img src="%PUBURL%/%WEB%/SharedImages/wip.gif"></td> <td valign="center"><b><font color="red" size=+2>Warning!</font><br><font size="+1">This page is under construction. The instructions are currently not complete!</font></b></td></tr></table>

---+ Mutual Information Support for RNA Secondary Structure Models

Predicting base interactions in RNA structures from the phylogenetic-significance of mutual information between columns.

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---++ Overview: What do these programs do?

Reference.

---++ Compile modified version of rate4site

The program <b>[[http://www.tau.ac.il/~itaymay/cp/rate4site.html][rate4site]]</b> is used to infer a phylogenetic tree with per-site substitution rates that generates the observed sequence alignment. In order to properly function on RNA alignments, <b>rate4site</b> required a minor source code modification to deal with gap characters as a separate state. For convenience, I have included this modification on the latest source release for download here.

| [[%ATTACHURL%/rate4site.tgz][%ICON{download}% Download <b>rate4site</b>]] | version 2.01 (Nov06) modified | 18 December 2008 |

The included Makefile is for compiling under Windows. To compile use this command instead:

<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
g++ -Dunix -o rate4site.exe -O3 *.cpp
</div></code>
This topic: Lab > ToolList > ToolsRNAStructureMutualInformation
Topic revision: r1 - 2008-12-18 - JeffreyBarrick