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Nucleic Acids Research Advance Access published online on June 3, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn283
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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xREI: a phylo-grammar visualization webserver

Lars Barquist* and Ian Holmes

Department of Bioengineering, University of California, Berkeley

*To whom correspondence should be addressed. Email: lbarquist{at}gmail.com

Received February 9, 2008. Revised April 16, 2008. Accepted April 26, 2008.

Phylo-grammars, probabilistic models combining Markov chain substitution models with stochastic grammars, are powerful models for annotating structured features in multiple sequence alignments and analyzing the evolution of those features. In the past, these methods have been cumbersome to implement and modify. xrate provides means for the rapid development of phylo-grammars (using a simple file format) and automated parameterization of those grammars from training data (via the Expectation Maximization algorithm). xREI (pron. ‘X-ray’) is an intuitive, flexible AJAX (Asynchronous Javascript And XML) web interface to xrate providing grammar visualization tools as well as access to xrate's training and annotation functionality. It is hoped that this application will serve as a valuable tool to those developing phylo-grammars, and as a means for the exploration and dissemination of such models. xREI is available at http://harmony.biowiki.org/xrei/


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