Phylo Grammars

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Phylo Grammars

A "phylo-grammar" is a stochastic grammar whose emissions (i.e. terminals) are alignment columns, typically generated by evolving a continuous-time Markov process on a phylogenetic tree.

As a class of models, phylo-grammars include all simple point substitution models (including e.g. codon substitution, conditional approximations to context-dependent substitution, etc). They also include HMM- and SCFG-like models for co-ordinated evolution of features and domains (e.g. exon/intron predictors, or autocorrelated models of ultraconserved genomic regions).

Notable bioinformatics programs that use phylo-grammars include Pfold, Phastcons, Exoniphy and Dless.

For references see the following pages