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Mutual Information Support for RNA Secondary Structure Models

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

Overview: What do these programs do?

Reference.

Install a modified version of rate4site

The program rate4site 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, rate4site 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.

Download rate4site

version 2.01 (Nov06) modified

18 December 2008

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

Finally, add the new rate4site executable to your $PATH so that the mutual information scripts can employ it.

Install the esl-weight program from Infernal

Chances are that you already have Infernal installed if you routinely work with RNA alignments. If not, download Infernal, compile, and install according to the included instructions.

Official Infernal Site

These scripts actually only need the weight or esl-weight utility program that is included. This program will be compiled, but may NOT be installed by default. For infernal-1.0rc5, you can find the binary at infernal-1.0rc5/easel/miniapps/esl-weight. Either move this into a bin directory or add it to your $PATH so that the mutual information scripts can employ it.