xREI: a phylo-grammar visualization webserver.

Abstract

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/