( grammar
( name poly-2N-unobserved )
;; flags
(parametric)
( update-rules 1 )
( update-rates 1 )
;; Nonterminal declarations and modifiers
(nonterminal (name Start))
(nonterminal (name Fwd1))
( pgroup
(
(p1death 0.001)
(p1stay 0.999)
))
(transform
(from (Start))
(to (Fwd1))
(prob 1.0))
;; Fwd -> ...
(transform
(from (Fwd1))
(to (POS Fwd1*))
(gaps-ok))
(transform
(from (Fwd1*))
(to ())
(prob p1death))
(transform
(from (Fwd1*))
(to (Fwd1))
(prob p1stay))
;; codon chain OBS
( chain
( terminal (POS) )
( update-policy parametric )
( initial ( state ( a ) ) ( prob ( 0.0 ) ) )
( initial ( state ( b ) ) ( prob ( Pb ) ) )
( initial ( state ( c ) ) ( prob ( Pc ) ) )
;; substitution rates
( mutate ( from ( a ) ) ( to ( a ) ) ( rate T ) )
( mutate ( from ( b ) ) ( to ( a ) ) ( rate T * 0.999 ) )
( mutate ( from ( b ) ) ( to ( b ) ) ( rate T * 0.001 ) )
( mutate ( from ( c ) ) ( to ( c ) ) ( rate T * 1 ) )
);;end chain OBS
;; parameters
( pgroup
((Pb 0.5)
(Pc 0.5))
)
;; end of pgroup
( rate
(T 1.0)
) ;; end of rate
;; end of params
) ;; end of grammar
( alphabet
( name RNA )
( token ( a b c ) )
(wildcard *)
) ;; end alphabet RNA