xREI

xREI provides probabilistic modeling and analysis of phylo-grammars that integrate Markov chain substitution models with stochastic grammars to annotate structured features in multiple sequence alignments and analyze their evolutionary trajectories.

Key Features:

• Phylo-grammar modeling: Integrates Markov chain substitution models with stochastic grammars to represent structural and phylogenetic variation in alignments.
• Visualization: Generates state transition graphs and substitution matrices for inspecting model structure and substitution processes.
• Grammar development and customization: Supports predefined and user-defined phylo-grammars via xrate's simple file format.
• Automated parameterization: Employs the Expectation Maximization algorithm to estimate grammar parameters from training data.
• Training and annotation: Provides functionality for using training datasets and producing annotations of structured features in multiple sequence alignments.
• xrate-based implementation: Builds on xrate to model both structural and phylogenetic variations in multiple sequence alignments.

Scientific Applications:

• Annotation of structured features: Annotates structured elements within multiple sequence alignments using phylo-grammars.
• Evolutionary analysis of structures: Analyzes the evolutionary trajectories and structural changes of sequence features over time.
• Model development for evolutionary hypotheses: Enables development and parameterization of phylo-grammars tailored to specific evolutionary questions using training data.

Methodology:

xREI uses xrate to combine Markov chain substitution models with stochastic grammars, models structural and phylogenetic variation in multiple sequence alignments, parameterizes grammars via the Expectation Maximization algorithm, and accepts grammar specifications in xrate's simple file format.