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