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;; Grammar CodeML_sn_f4x3
;;
(grammar
(name CodeML_sn_f4x3)
(parametric)
(update-rates 1)
(update-rules 1)
;; Nonterminal declarations and modifiers
(nonterminal (name START))
(nonterminal (name EMIT))
;; Transformation rules for grammar symbols
;; Nonterminal START
;;
(transform (from (START)) (to ()) (prob ~ext))
(transform (from (START)) (to (EMIT)) (prob ext))
;; Nonterminal EMIT
;;
(transform (from (EMIT)) (to (COD0 COD1 COD2 EMIT*)) (gaps-ok))
(transform (from (EMIT*)) (to ()) (prob ~ext))
(transform (from (EMIT*)) (to (EMIT)) (prob ext))
;; Probability and rate parameters
(pgroup
((ext 0.5)
(~ext 0.5))
((pa0 0.25)
(pc0 0.25)
(pg0 0.25)
(pt0 0.25))
((pa1 0.25)
(pc1 0.25)
(pg1 0.25)
(pt1 0.25))
((pa2 0.25)
(pc2 0.25)
(pg2 0.25)
(pt2 0.25))
((k 0.5)
(~k 0.5))
) ;; end pgroup
(rate
(s 1)
(n 1)
) ;; end rate
;; Markov chain substitution models
(chain
(update-policy parametric)
(terminal (COD0 COD1 COD2))
;; initial probability distribution
(initial (state (a a a)) (prob pa0 * pa1 * pa2))
(initial (state (c a a)) (prob pc0 * pa1 * pa2))
(initial (state (g a a)) (prob pg0 * pa1 * pa2))
(initial (state (a c a)) (prob pa0 * pc1 * pa2))
(initial (state (c c a)) (prob pc0 * pc1 * pa2))
(initial (state (g c a)) (prob pg0 * pc1 * pa2))
(initial (state (t c a)) (prob pt0 * pc1 * pa2))
(initial (state (a g a)) (prob pa0 * pg1 * pa2))
(initial (state (c g a)) (prob pc0 * pg1 * pa2))
(initial (state (g g a)) (prob pg0 * pg1 * pa2))
(initial (state (a t a)) (prob pa0 * pt1 * pa2))
(initial (state (c t a)) (prob pc0 * pt1 * pa2))
(initial (state (g t a)) (prob pg0 * pt1 * pa2))
(initial (state (t t a)) (prob pt0 * pt1 * pa2))
(initial (state (a a c)) (prob pa0 * pa1 * pc2))
(initial (state (c a c)) (prob pc0 * pa1 * pc2))
(initial (state (g a c)) (prob pg0 * pa1 * pc2))
(initial (state (t a c)) (prob pt0 * pa1 * pc2))
(initial (state (a c c)) (prob pa0 * pc1 * pc2))
(initial (state (c c c)) (prob pc0 * pc1 * pc2))
(initial (state (g c c)) (prob pg0 * pc1 * pc2))
(initial (state (t c c)) (prob pt0 * pc1 * pc2))
(initial (state (a g c)) (prob pa0 * pg1 * pc2))
(initial (state (c g c)) (prob pc0 * pg1 * pc2))
(initial (state (g g c)) (prob pg0 * pg1 * pc2))
(initial (state (t g c)) (prob pt0 * pg1 * pc2))
(initial (state (a t c)) (prob pa0 * pt1 * pc2))
(initial (state (c t c)) (prob pc0 * pt1 * pc2))
(initial (state (g t c)) (prob pg0 * pt1 * pc2))
(initial (state (t t c)) (prob pt0 * pt1 * pc2))
(initial (state (a a g)) (prob pa0 * pa1 * pg2))
(initial (state (c a g)) (prob pc0 * pa1 * pg2))
(initial (state (g a g)) (prob pg0 * pa1 * pg2))
(initial (state (a c g)) (prob pa0 * pc1 * pg2))
(initial (state (c c g)) (prob pc0 * pc1 * pg2))
(initial (state (g c g)) (prob pg0 * pc1 * pg2))
(initial (state (t c g)) (prob pt0 * pc1 * pg2))
(initial (state (a g g)) (prob pa0 * pg1 * pg2))
(initial (state (c g g)) (prob pc0 * pg1 * pg2))
(initial (state (g g g)) (prob pg0 * pg1 * pg2))
(initial (state (t g g)) (prob pt0 * pg1 * pg2))
(initial (state (a t g)) (prob pa0 * pt1 * pg2))
(initial (state (c t g)) (prob pc0 * pt1 * pg2))
(initial (state (g t g)) (prob pg0 * pt1 * pg2))
(initial (state (t t g)) (prob pt0 * pt1 * pg2))
(initial (state (a a t)) (prob pa0 * pa1 * pt2))
(initial (state (c a t)) (prob pc0 * pa1 * pt2))
(initial (state (g a t)) (prob pg0 * pa1 * pt2))
(initial (state (t a t)) (prob pt0 * pa1 * pt2))
(initial (state (a c t)) (prob pa0 * pc1 * pt2))
(initial (state (c c t)) (prob pc0 * pc1 * pt2))
(initial (state (g c t)) (prob pg0 * pc1 * pt2))
(initial (state (t c t)) (prob pt0 * pc1 * pt2))
(initial (state (a g t)) (prob pa0 * pg1 * pt2))
(initial (state (c g t)) (prob pc0 * pg1 * pt2))
(initial (state (g g t)) (prob pg0 * pg1 * pt2))
(initial (state (t g t)) (prob pt0 * pg1 * pt2))
(initial (state (a t t)) (prob pa0 * pt1 * pt2))
(initial (state (c t t)) (prob pc0 * pt1 * pt2))
(initial (state (g t t)) (prob pg0 * pt1 * pt2))
(initial (state (t t t)) (prob pt0 * pt1 * pt2))
;; mutation rates
(mutate (from (a a a)) (to (a a a)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pa2) + (const pa0) * (const pc1) * (const pa2) + (const pa0) * (const pt1) * (const pa2) + (const pa0) * (const pa1) * (const pc2) + (const pa0) * (const pa1) * (const pt2))))
(mutate (from (a a a)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (a a a)) (to (g a a)) (rate n * pg0 * pa1 * pa2))
(mutate (from (a a a)) (to (a c a)) (rate n * pa0 * pc1 * pa2 * k))
(mutate (from (a a a)) (to (a g a)) (rate n * pa0 * pg1 * pa2))
(mutate (from (a a a)) (to (a t a)) (rate n * pa0 * pt1 * pa2 * k))
(mutate (from (a a a)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (a a a)) (to (a a g)) (rate s * pa0 * pa1 * pg2))
(mutate (from (a a a)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (c a a)) (to (a a a)) (rate n * pa0 * pa1 * pa2 * k))
(mutate (from (c a a)) (to (c a a)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pa2) + (const pg0) * (const pa1) * (const pa2) + (const pc0) * (const pc1) * (const pa2) + (const pc0) * (const pt1) * (const pa2) + (const pc0) * (const pa1) * (const pc2) + (const pc0) * (const pa1) * (const pt2))))
(mutate (from (c a a)) (to (g a a)) (rate n * pg0 * pa1 * pa2 * k))
(mutate (from (c a a)) (to (c c a)) (rate n * pc0 * pc1 * pa2 * k))
(mutate (from (c a a)) (to (c g a)) (rate n * pc0 * pg1 * pa2))
(mutate (from (c a a)) (to (c t a)) (rate n * pc0 * pt1 * pa2 * k))
(mutate (from (c a a)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (c a a)) (to (c a g)) (rate s * pc0 * pa1 * pg2))
(mutate (from (c a a)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (g a a)) (to (a a a)) (rate n * pa0 * pa1 * pa2))
(mutate (from (g a a)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (g a a)) (to (g a a)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pa2) + (const pg0) * (const pc1) * (const pa2) + (const pg0) * (const pt1) * (const pa2) + (const pg0) * (const pa1) * (const pc2) + (const pg0) * (const pa1) * (const pt2))))
(mutate (from (g a a)) (to (g c a)) (rate n * pg0 * pc1 * pa2 * k))
(mutate (from (g a a)) (to (g g a)) (rate n * pg0 * pg1 * pa2))
(mutate (from (g a a)) (to (g t a)) (rate n * pg0 * pt1 * pa2 * k))
(mutate (from (g a a)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (g a a)) (to (g a g)) (rate s * pg0 * pa1 * pg2))
(mutate (from (g a a)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (a c a)) (to (a a a)) (rate n * pa0 * pa1 * pa2 * k))
(mutate (from (a c a)) (to (a c a)) (rate ~k * ((const s) * ((const pa0) * (const pc1) * (const pc2) + (const pa0) * (const pc1) * (const pt2)) + (const n) * ((const pc0) * (const pc1) * (const pa2) + (const pt0) * (const pc1) * (const pa2) + (const pa0) * (const pa1) * (const pa2) + (const pa0) * (const pg1) * (const pa2)))))
(mutate (from (a c a)) (to (c c a)) (rate n * pc0 * pc1 * pa2 * k))
(mutate (from (a c a)) (to (g c a)) (rate n * pg0 * pc1 * pa2))
(mutate (from (a c a)) (to (t c a)) (rate n * pt0 * pc1 * pa2 * k))
(mutate (from (a c a)) (to (a g a)) (rate n * pa0 * pg1 * pa2 * k))
(mutate (from (a c a)) (to (a t a)) (rate n * pa0 * pt1 * pa2))
(mutate (from (a c a)) (to (a c c)) (rate s * pa0 * pc1 * pc2 * k))
(mutate (from (a c a)) (to (a c g)) (rate s * pa0 * pc1 * pg2))
(mutate (from (a c a)) (to (a c t)) (rate s * pa0 * pc1 * pt2 * k))
(mutate (from (c c a)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (c c a)) (to (a c a)) (rate n * pa0 * pc1 * pa2 * k))
(mutate (from (c c a)) (to (c c a)) (rate ~k * ((const s) * ((const pc0) * (const pc1) * (const pc2) + (const pc0) * (const pc1) * (const pt2)) + (const n) * ((const pa0) * (const pc1) * (const pa2) + (const pg0) * (const pc1) * (const pa2) + (const pc0) * (const pa1) * (const pa2) + (const pc0) * (const pg1) * (const pa2)))))
(mutate (from (c c a)) (to (g c a)) (rate n * pg0 * pc1 * pa2 * k))
(mutate (from (c c a)) (to (t c a)) (rate n * pt0 * pc1 * pa2))
(mutate (from (c c a)) (to (c g a)) (rate n * pc0 * pg1 * pa2 * k))
(mutate (from (c c a)) (to (c t a)) (rate n * pc0 * pt1 * pa2))
(mutate (from (c c a)) (to (c c c)) (rate s * pc0 * pc1 * pc2 * k))
(mutate (from (c c a)) (to (c c g)) (rate s * pc0 * pc1 * pg2))
(mutate (from (c c a)) (to (c c t)) (rate s * pc0 * pc1 * pt2 * k))
(mutate (from (g c a)) (to (g a a)) (rate n * pg0 * pa1 * pa2 * k))
(mutate (from (g c a)) (to (a c a)) (rate n * pa0 * pc1 * pa2))
(mutate (from (g c a)) (to (c c a)) (rate n * pc0 * pc1 * pa2 * k))
(mutate (from (g c a)) (to (g c a)) (rate ~k * ((const s) * ((const pg0) * (const pc1) * (const pc2) + (const pg0) * (const pc1) * (const pt2)) + (const n) * ((const pc0) * (const pc1) * (const pa2) + (const pt0) * (const pc1) * (const pa2) + (const pg0) * (const pa1) * (const pa2) + (const pg0) * (const pg1) * (const pa2)))))
(mutate (from (g c a)) (to (t c a)) (rate n * pt0 * pc1 * pa2 * k))
(mutate (from (g c a)) (to (g g a)) (rate n * pg0 * pg1 * pa2 * k))
(mutate (from (g c a)) (to (g t a)) (rate n * pg0 * pt1 * pa2))
(mutate (from (g c a)) (to (g c c)) (rate s * pg0 * pc1 * pc2 * k))
(mutate (from (g c a)) (to (g c g)) (rate s * pg0 * pc1 * pg2))
(mutate (from (g c a)) (to (g c t)) (rate s * pg0 * pc1 * pt2 * k))
(mutate (from (t c a)) (to (a c a)) (rate n * pa0 * pc1 * pa2 * k))
(mutate (from (t c a)) (to (c c a)) (rate n * pc0 * pc1 * pa2))
(mutate (from (t c a)) (to (g c a)) (rate n * pg0 * pc1 * pa2 * k))
(mutate (from (t c a)) (to (t c a)) (rate ~k * ((const s) * ((const pt0) * (const pc1) * (const pc2) + (const pt0) * (const pc1) * (const pt2)) + (const n) * ((const pa0) * (const pc1) * (const pa2) + (const pg0) * (const pc1) * (const pa2)))))
(mutate (from (t c a)) (to (t t a)) (rate n * pt0 * pt1 * pa2))
(mutate (from (t c a)) (to (t c c)) (rate s * pt0 * pc1 * pc2 * k))
(mutate (from (t c a)) (to (t c g)) (rate s * pt0 * pc1 * pg2))
(mutate (from (t c a)) (to (t c t)) (rate s * pt0 * pc1 * pt2 * k))
(mutate (from (a g a)) (to (a a a)) (rate n * pa0 * pa1 * pa2))
(mutate (from (a g a)) (to (a c a)) (rate n * pa0 * pc1 * pa2 * k))
(mutate (from (a g a)) (to (a g a)) (rate ~k * ((const s) * (const pc0) * (const pg1) * (const pa2) + (const n) * ((const pa0) * (const pc1) * (const pa2) + (const pa0) * (const pt1) * (const pa2) + (const pa0) * (const pg1) * (const pc2) + (const pa0) * (const pg1) * (const pt2)))))
(mutate (from (a g a)) (to (c g a)) (rate s * pc0 * pg1 * pa2 * k))
(mutate (from (a g a)) (to (g g a)) (rate n * pg0 * pg1 * pa2))
(mutate (from (a g a)) (to (a t a)) (rate n * pa0 * pt1 * pa2 * k))
(mutate (from (a g a)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (a g a)) (to (a g g)) (rate s * pa0 * pg1 * pg2))
(mutate (from (a g a)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (c g a)) (to (c a a)) (rate n * pc0 * pa1 * pa2))
(mutate (from (c g a)) (to (c c a)) (rate n * pc0 * pc1 * pa2 * k))
(mutate (from (c g a)) (to (a g a)) (rate s * pa0 * pg1 * pa2 * k))
(mutate (from (c g a)) (to (c g a)) (rate ~k * ((const s) * ((const pa0) * (const pg1) * (const pa2) + (const pc0) * (const pg1) * (const pc2) + (const pc0) * (const pg1) * (const pt2)) + (const n) * ((const pg0) * (const pg1) * (const pa2) + (const pc0) * (const pc1) * (const pa2) + (const pc0) * (const pt1) * (const pa2)))))
(mutate (from (c g a)) (to (g g a)) (rate n * pg0 * pg1 * pa2 * k))
(mutate (from (c g a)) (to (c t a)) (rate n * pc0 * pt1 * pa2 * k))
(mutate (from (c g a)) (to (c g c)) (rate s * pc0 * pg1 * pc2 * k))
(mutate (from (c g a)) (to (c g g)) (rate s * pc0 * pg1 * pg2))
(mutate (from (c g a)) (to (c g t)) (rate s * pc0 * pg1 * pt2 * k))
(mutate (from (g g a)) (to (g a a)) (rate n * pg0 * pa1 * pa2))
(mutate (from (g g a)) (to (g c a)) (rate n * pg0 * pc1 * pa2 * k))
(mutate (from (g g a)) (to (a g a)) (rate n * pa0 * pg1 * pa2))
(mutate (from (g g a)) (to (c g a)) (rate n * pc0 * pg1 * pa2 * k))
(mutate (from (g g a)) (to (g g a)) (rate ~k * ((const s) * ((const pg0) * (const pg1) * (const pc2) + (const pg0) * (const pg1) * (const pt2)) + (const n) * ((const pc0) * (const pg1) * (const pa2) + (const pg0) * (const pc1) * (const pa2) + (const pg0) * (const pt1) * (const pa2)))))
(mutate (from (g g a)) (to (g t a)) (rate n * pg0 * pt1 * pa2 * k))
(mutate (from (g g a)) (to (g g c)) (rate s * pg0 * pg1 * pc2 * k))
(mutate (from (g g a)) (to (g g g)) (rate s * pg0 * pg1 * pg2))
(mutate (from (g g a)) (to (g g t)) (rate s * pg0 * pg1 * pt2 * k))
(mutate (from (a t a)) (to (a a a)) (rate n * pa0 * pa1 * pa2 * k))
(mutate (from (a t a)) (to (a c a)) (rate n * pa0 * pc1 * pa2))
(mutate (from (a t a)) (to (a g a)) (rate n * pa0 * pg1 * pa2 * k))
(mutate (from (a t a)) (to (a t a)) (rate ~k * ((const s) * ((const pa0) * (const pt1) * (const pc2) + (const pa0) * (const pt1) * (const pt2)) + (const n) * ((const pc0) * (const pt1) * (const pa2) + (const pt0) * (const pt1) * (const pa2) + (const pa0) * (const pa1) * (const pa2) + (const pa0) * (const pg1) * (const pa2)))))
(mutate (from (a t a)) (to (c t a)) (rate n * pc0 * pt1 * pa2 * k))
(mutate (from (a t a)) (to (g t a)) (rate n * pg0 * pt1 * pa2))
(mutate (from (a t a)) (to (t t a)) (rate n * pt0 * pt1 * pa2 * k))
(mutate (from (a t a)) (to (a t c)) (rate s * pa0 * pt1 * pc2 * k))
(mutate (from (a t a)) (to (a t g)) (rate n * pa0 * pt1 * pg2))
(mutate (from (a t a)) (to (a t t)) (rate s * pa0 * pt1 * pt2 * k))
(mutate (from (c t a)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (c t a)) (to (c c a)) (rate n * pc0 * pc1 * pa2))
(mutate (from (c t a)) (to (c g a)) (rate n * pc0 * pg1 * pa2 * k))
(mutate (from (c t a)) (to (a t a)) (rate n * pa0 * pt1 * pa2 * k))
(mutate (from (c t a)) (to (c t a)) (rate ~k * ((const s) * ((const pc0) * (const pt1) * (const pc2) + (const pc0) * (const pt1) * (const pt2)) + (const n) * ((const pa0) * (const pt1) * (const pa2) + (const pg0) * (const pt1) * (const pa2) + (const pc0) * (const pa1) * (const pa2) + (const pc0) * (const pg1) * (const pa2)))))
(mutate (from (c t a)) (to (g t a)) (rate n * pg0 * pt1 * pa2 * k))
(mutate (from (c t a)) (to (t t a)) (rate s * pt0 * pt1 * pa2))
(mutate (from (c t a)) (to (c t c)) (rate s * pc0 * pt1 * pc2 * k))
(mutate (from (c t a)) (to (c t g)) (rate s * pc0 * pt1 * pg2))
(mutate (from (c t a)) (to (c t t)) (rate s * pc0 * pt1 * pt2 * k))
(mutate (from (g t a)) (to (g a a)) (rate n * pg0 * pa1 * pa2 * k))
(mutate (from (g t a)) (to (g c a)) (rate n * pg0 * pc1 * pa2))
(mutate (from (g t a)) (to (g g a)) (rate n * pg0 * pg1 * pa2 * k))
(mutate (from (g t a)) (to (a t a)) (rate n * pa0 * pt1 * pa2))
(mutate (from (g t a)) (to (c t a)) (rate n * pc0 * pt1 * pa2 * k))
(mutate (from (g t a)) (to (g t a)) (rate ~k * ((const s) * ((const pg0) * (const pt1) * (const pc2) + (const pg0) * (const pt1) * (const pt2)) + (const n) * ((const pc0) * (const pt1) * (const pa2) + (const pt0) * (const pt1) * (const pa2) + (const pg0) * (const pa1) * (const pa2) + (const pg0) * (const pg1) * (const pa2)))))
(mutate (from (g t a)) (to (t t a)) (rate n * pt0 * pt1 * pa2 * k))
(mutate (from (g t a)) (to (g t c)) (rate s * pg0 * pt1 * pc2 * k))
(mutate (from (g t a)) (to (g t g)) (rate s * pg0 * pt1 * pg2))
(mutate (from (g t a)) (to (g t t)) (rate s * pg0 * pt1 * pt2 * k))
(mutate (from (t t a)) (to (t c a)) (rate n * pt0 * pc1 * pa2))
(mutate (from (t t a)) (to (a t a)) (rate n * pa0 * pt1 * pa2 * k))
(mutate (from (t t a)) (to (c t a)) (rate s * pc0 * pt1 * pa2))
(mutate (from (t t a)) (to (g t a)) (rate n * pg0 * pt1 * pa2 * k))
(mutate (from (t t a)) (to (t t a)) (rate ~k * (const n) * ((const pa0) * (const pt1) * (const pa2) + (const pg0) * (const pt1) * (const pa2) + (const pt0) * (const pt1) * (const pc2) + (const pt0) * (const pt1) * (const pt2))))
(mutate (from (t t a)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (t t a)) (to (t t g)) (rate s * pt0 * pt1 * pg2))
(mutate (from (t t a)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (a a c)) (to (a a a)) (rate n * pa0 * pa1 * pa2 * k))
(mutate (from (a a c)) (to (a a c)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pc2) + (const pt0) * (const pa1) * (const pc2) + (const pa0) * (const pc1) * (const pc2) + (const pa0) * (const pt1) * (const pc2) + (const pa0) * (const pa1) * (const pa2) + (const pa0) * (const pa1) * (const pg2))))
(mutate (from (a a c)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (a a c)) (to (g a c)) (rate n * pg0 * pa1 * pc2))
(mutate (from (a a c)) (to (t a c)) (rate n * pt0 * pa1 * pc2 * k))
(mutate (from (a a c)) (to (a c c)) (rate n * pa0 * pc1 * pc2 * k))
(mutate (from (a a c)) (to (a g c)) (rate n * pa0 * pg1 * pc2))
(mutate (from (a a c)) (to (a t c)) (rate n * pa0 * pt1 * pc2 * k))
(mutate (from (a a c)) (to (a a g)) (rate n * pa0 * pa1 * pg2 * k))
(mutate (from (a a c)) (to (a a t)) (rate s * pa0 * pa1 * pt2))
(mutate (from (c a c)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (c a c)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (c a c)) (to (c a c)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pc2) + (const pg0) * (const pa1) * (const pc2) + (const pc0) * (const pc1) * (const pc2) + (const pc0) * (const pt1) * (const pc2) + (const pc0) * (const pa1) * (const pa2) + (const pc0) * (const pa1) * (const pg2))))
(mutate (from (c a c)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (c a c)) (to (t a c)) (rate n * pt0 * pa1 * pc2))
(mutate (from (c a c)) (to (c c c)) (rate n * pc0 * pc1 * pc2 * k))
(mutate (from (c a c)) (to (c g c)) (rate n * pc0 * pg1 * pc2))
(mutate (from (c a c)) (to (c t c)) (rate n * pc0 * pt1 * pc2 * k))
(mutate (from (c a c)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (c a c)) (to (c a t)) (rate s * pc0 * pa1 * pt2))
(mutate (from (g a c)) (to (g a a)) (rate n * pg0 * pa1 * pa2 * k))
(mutate (from (g a c)) (to (a a c)) (rate n * pa0 * pa1 * pc2))
(mutate (from (g a c)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (g a c)) (to (g a c)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pc2) + (const pt0) * (const pa1) * (const pc2) + (const pg0) * (const pc1) * (const pc2) + (const pg0) * (const pt1) * (const pc2) + (const pg0) * (const pa1) * (const pa2) + (const pg0) * (const pa1) * (const pg2))))
(mutate (from (g a c)) (to (t a c)) (rate n * pt0 * pa1 * pc2 * k))
(mutate (from (g a c)) (to (g c c)) (rate n * pg0 * pc1 * pc2 * k))
(mutate (from (g a c)) (to (g g c)) (rate n * pg0 * pg1 * pc2))
(mutate (from (g a c)) (to (g t c)) (rate n * pg0 * pt1 * pc2 * k))
(mutate (from (g a c)) (to (g a g)) (rate n * pg0 * pa1 * pg2 * k))
(mutate (from (g a c)) (to (g a t)) (rate s * pg0 * pa1 * pt2))
(mutate (from (t a c)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (t a c)) (to (c a c)) (rate n * pc0 * pa1 * pc2))
(mutate (from (t a c)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (t a c)) (to (t a c)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pc2) + (const pg0) * (const pa1) * (const pc2) + (const pt0) * (const pc1) * (const pc2) + (const pt0) * (const pt1) * (const pc2))))
(mutate (from (t a c)) (to (t c c)) (rate n * pt0 * pc1 * pc2 * k))
(mutate (from (t a c)) (to (t g c)) (rate n * pt0 * pg1 * pc2))
(mutate (from (t a c)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (t a c)) (to (t a t)) (rate s * pt0 * pa1 * pt2))
(mutate (from (a c c)) (to (a c a)) (rate s * pa0 * pc1 * pa2 * k))
(mutate (from (a c c)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (a c c)) (to (a c c)) (rate ~k * ((const s) * ((const pa0) * (const pc1) * (const pa2) + (const pa0) * (const pc1) * (const pg2)) + (const n) * ((const pc0) * (const pc1) * (const pc2) + (const pt0) * (const pc1) * (const pc2) + (const pa0) * (const pa1) * (const pc2) + (const pa0) * (const pg1) * (const pc2)))))
(mutate (from (a c c)) (to (c c c)) (rate n * pc0 * pc1 * pc2 * k))
(mutate (from (a c c)) (to (g c c)) (rate n * pg0 * pc1 * pc2))
(mutate (from (a c c)) (to (t c c)) (rate n * pt0 * pc1 * pc2 * k))
(mutate (from (a c c)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (a c c)) (to (a t c)) (rate n * pa0 * pt1 * pc2))
(mutate (from (a c c)) (to (a c g)) (rate s * pa0 * pc1 * pg2 * k))
(mutate (from (a c c)) (to (a c t)) (rate s * pa0 * pc1 * pt2))
(mutate (from (c c c)) (to (c c a)) (rate s * pc0 * pc1 * pa2 * k))
(mutate (from (c c c)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (c c c)) (to (a c c)) (rate n * pa0 * pc1 * pc2 * k))
(mutate (from (c c c)) (to (c c c)) (rate ~k * ((const s) * ((const pc0) * (const pc1) * (const pa2) + (const pc0) * (const pc1) * (const pg2)) + (const n) * ((const pa0) * (const pc1) * (const pc2) + (const pg0) * (const pc1) * (const pc2) + (const pc0) * (const pa1) * (const pc2) + (const pc0) * (const pg1) * (const pc2)))))
(mutate (from (c c c)) (to (g c c)) (rate n * pg0 * pc1 * pc2 * k))
(mutate (from (c c c)) (to (t c c)) (rate n * pt0 * pc1 * pc2))
(mutate (from (c c c)) (to (c g c)) (rate n * pc0 * pg1 * pc2 * k))
(mutate (from (c c c)) (to (c t c)) (rate n * pc0 * pt1 * pc2))
(mutate (from (c c c)) (to (c c g)) (rate s * pc0 * pc1 * pg2 * k))
(mutate (from (c c c)) (to (c c t)) (rate s * pc0 * pc1 * pt2))
(mutate (from (g c c)) (to (g c a)) (rate s * pg0 * pc1 * pa2 * k))
(mutate (from (g c c)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (g c c)) (to (a c c)) (rate n * pa0 * pc1 * pc2))
(mutate (from (g c c)) (to (c c c)) (rate n * pc0 * pc1 * pc2 * k))
(mutate (from (g c c)) (to (g c c)) (rate ~k * ((const s) * ((const pg0) * (const pc1) * (const pa2) + (const pg0) * (const pc1) * (const pg2)) + (const n) * ((const pc0) * (const pc1) * (const pc2) + (const pt0) * (const pc1) * (const pc2) + (const pg0) * (const pa1) * (const pc2) + (const pg0) * (const pg1) * (const pc2)))))
(mutate (from (g c c)) (to (t c c)) (rate n * pt0 * pc1 * pc2 * k))
(mutate (from (g c c)) (to (g g c)) (rate n * pg0 * pg1 * pc2 * k))
(mutate (from (g c c)) (to (g t c)) (rate n * pg0 * pt1 * pc2))
(mutate (from (g c c)) (to (g c g)) (rate s * pg0 * pc1 * pg2 * k))
(mutate (from (g c c)) (to (g c t)) (rate s * pg0 * pc1 * pt2))
(mutate (from (t c c)) (to (t c a)) (rate s * pt0 * pc1 * pa2 * k))
(mutate (from (t c c)) (to (t a c)) (rate n * pt0 * pa1 * pc2 * k))
(mutate (from (t c c)) (to (a c c)) (rate n * pa0 * pc1 * pc2 * k))
(mutate (from (t c c)) (to (c c c)) (rate n * pc0 * pc1 * pc2))
(mutate (from (t c c)) (to (g c c)) (rate n * pg0 * pc1 * pc2 * k))
(mutate (from (t c c)) (to (t c c)) (rate ~k * ((const s) * ((const pt0) * (const pc1) * (const pa2) + (const pt0) * (const pc1) * (const pg2)) + (const n) * ((const pa0) * (const pc1) * (const pc2) + (const pg0) * (const pc1) * (const pc2) + (const pt0) * (const pa1) * (const pc2) + (const pt0) * (const pg1) * (const pc2)))))
(mutate (from (t c c)) (to (t g c)) (rate n * pt0 * pg1 * pc2 * k))
(mutate (from (t c c)) (to (t t c)) (rate n * pt0 * pt1 * pc2))
(mutate (from (t c c)) (to (t c g)) (rate s * pt0 * pc1 * pg2 * k))
(mutate (from (t c c)) (to (t c t)) (rate s * pt0 * pc1 * pt2))
(mutate (from (a g c)) (to (a g a)) (rate n * pa0 * pg1 * pa2 * k))
(mutate (from (a g c)) (to (a a c)) (rate n * pa0 * pa1 * pc2))
(mutate (from (a g c)) (to (a c c)) (rate n * pa0 * pc1 * pc2 * k))
(mutate (from (a g c)) (to (a g c)) (rate ~k * (const n) * ((const pc0) * (const pg1) * (const pc2) + (const pt0) * (const pg1) * (const pc2) + (const pa0) * (const pc1) * (const pc2) + (const pa0) * (const pt1) * (const pc2) + (const pa0) * (const pg1) * (const pa2) + (const pa0) * (const pg1) * (const pg2))))
(mutate (from (a g c)) (to (c g c)) (rate n * pc0 * pg1 * pc2 * k))
(mutate (from (a g c)) (to (g g c)) (rate n * pg0 * pg1 * pc2))
(mutate (from (a g c)) (to (t g c)) (rate n * pt0 * pg1 * pc2 * k))
(mutate (from (a g c)) (to (a t c)) (rate n * pa0 * pt1 * pc2 * k))
(mutate (from (a g c)) (to (a g g)) (rate n * pa0 * pg1 * pg2 * k))
(mutate (from (a g c)) (to (a g t)) (rate s * pa0 * pg1 * pt2))
(mutate (from (c g c)) (to (c g a)) (rate s * pc0 * pg1 * pa2 * k))
(mutate (from (c g c)) (to (c a c)) (rate n * pc0 * pa1 * pc2))
(mutate (from (c g c)) (to (c c c)) (rate n * pc0 * pc1 * pc2 * k))
(mutate (from (c g c)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (c g c)) (to (c g c)) (rate ~k * ((const s) * ((const pc0) * (const pg1) * (const pa2) + (const pc0) * (const pg1) * (const pg2)) + (const n) * ((const pa0) * (const pg1) * (const pc2) + (const pg0) * (const pg1) * (const pc2) + (const pc0) * (const pc1) * (const pc2) + (const pc0) * (const pt1) * (const pc2)))))
(mutate (from (c g c)) (to (g g c)) (rate n * pg0 * pg1 * pc2 * k))
(mutate (from (c g c)) (to (t g c)) (rate n * pt0 * pg1 * pc2))
(mutate (from (c g c)) (to (c t c)) (rate n * pc0 * pt1 * pc2 * k))
(mutate (from (c g c)) (to (c g g)) (rate s * pc0 * pg1 * pg2 * k))
(mutate (from (c g c)) (to (c g t)) (rate s * pc0 * pg1 * pt2))
(mutate (from (g g c)) (to (g g a)) (rate s * pg0 * pg1 * pa2 * k))
(mutate (from (g g c)) (to (g a c)) (rate n * pg0 * pa1 * pc2))
(mutate (from (g g c)) (to (g c c)) (rate n * pg0 * pc1 * pc2 * k))
(mutate (from (g g c)) (to (a g c)) (rate n * pa0 * pg1 * pc2))
(mutate (from (g g c)) (to (c g c)) (rate n * pc0 * pg1 * pc2 * k))
(mutate (from (g g c)) (to (g g c)) (rate ~k * ((const s) * ((const pg0) * (const pg1) * (const pa2) + (const pg0) * (const pg1) * (const pg2)) + (const n) * ((const pc0) * (const pg1) * (const pc2) + (const pt0) * (const pg1) * (const pc2) + (const pg0) * (const pc1) * (const pc2) + (const pg0) * (const pt1) * (const pc2)))))
(mutate (from (g g c)) (to (t g c)) (rate n * pt0 * pg1 * pc2 * k))
(mutate (from (g g c)) (to (g t c)) (rate n * pg0 * pt1 * pc2 * k))
(mutate (from (g g c)) (to (g g g)) (rate s * pg0 * pg1 * pg2 * k))
(mutate (from (g g c)) (to (g g t)) (rate s * pg0 * pg1 * pt2))
(mutate (from (t g c)) (to (t a c)) (rate n * pt0 * pa1 * pc2))
(mutate (from (t g c)) (to (t c c)) (rate n * pt0 * pc1 * pc2 * k))
(mutate (from (t g c)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (t g c)) (to (c g c)) (rate n * pc0 * pg1 * pc2))
(mutate (from (t g c)) (to (g g c)) (rate n * pg0 * pg1 * pc2 * k))
(mutate (from (t g c)) (to (t g c)) (rate ~k * (const n) * ((const pa0) * (const pg1) * (const pc2) + (const pg0) * (const pg1) * (const pc2) + (const pt0) * (const pc1) * (const pc2) + (const pt0) * (const pt1) * (const pc2) + (const pt0) * (const pg1) * (const pg2))))
(mutate (from (t g c)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (t g c)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (t g c)) (to (t g t)) (rate s * pt0 * pg1 * pt2))
(mutate (from (a t c)) (to (a t a)) (rate s * pa0 * pt1 * pa2 * k))
(mutate (from (a t c)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (a t c)) (to (a c c)) (rate n * pa0 * pc1 * pc2))
(mutate (from (a t c)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (a t c)) (to (a t c)) (rate ~k * ((const s) * (const pa0) * (const pt1) * (const pa2) + (const n) * ((const pc0) * (const pt1) * (const pc2) + (const pt0) * (const pt1) * (const pc2) + (const pa0) * (const pa1) * (const pc2) + (const pa0) * (const pg1) * (const pc2) + (const pa0) * (const pt1) * (const pg2)))))
(mutate (from (a t c)) (to (c t c)) (rate n * pc0 * pt1 * pc2 * k))
(mutate (from (a t c)) (to (g t c)) (rate n * pg0 * pt1 * pc2))
(mutate (from (a t c)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (a t c)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (a t c)) (to (a t t)) (rate s * pa0 * pt1 * pt2))
(mutate (from (c t c)) (to (c t a)) (rate s * pc0 * pt1 * pa2 * k))
(mutate (from (c t c)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (c t c)) (to (c c c)) (rate n * pc0 * pc1 * pc2))
(mutate (from (c t c)) (to (c g c)) (rate n * pc0 * pg1 * pc2 * k))
(mutate (from (c t c)) (to (a t c)) (rate n * pa0 * pt1 * pc2 * k))
(mutate (from (c t c)) (to (c t c)) (rate ~k * ((const s) * ((const pc0) * (const pt1) * (const pa2) + (const pc0) * (const pt1) * (const pg2)) + (const n) * ((const pa0) * (const pt1) * (const pc2) + (const pg0) * (const pt1) * (const pc2) + (const pc0) * (const pa1) * (const pc2) + (const pc0) * (const pg1) * (const pc2)))))
(mutate (from (c t c)) (to (g t c)) (rate n * pg0 * pt1 * pc2 * k))
(mutate (from (c t c)) (to (t t c)) (rate n * pt0 * pt1 * pc2))
(mutate (from (c t c)) (to (c t g)) (rate s * pc0 * pt1 * pg2 * k))
(mutate (from (c t c)) (to (c t t)) (rate s * pc0 * pt1 * pt2))
(mutate (from (g t c)) (to (g t a)) (rate s * pg0 * pt1 * pa2 * k))
(mutate (from (g t c)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (g t c)) (to (g c c)) (rate n * pg0 * pc1 * pc2))
(mutate (from (g t c)) (to (g g c)) (rate n * pg0 * pg1 * pc2 * k))
(mutate (from (g t c)) (to (a t c)) (rate n * pa0 * pt1 * pc2))
(mutate (from (g t c)) (to (c t c)) (rate n * pc0 * pt1 * pc2 * k))
(mutate (from (g t c)) (to (g t c)) (rate ~k * ((const s) * ((const pg0) * (const pt1) * (const pa2) + (const pg0) * (const pt1) * (const pg2)) + (const n) * ((const pc0) * (const pt1) * (const pc2) + (const pt0) * (const pt1) * (const pc2) + (const pg0) * (const pa1) * (const pc2) + (const pg0) * (const pg1) * (const pc2)))))
(mutate (from (g t c)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (g t c)) (to (g t g)) (rate s * pg0 * pt1 * pg2 * k))
(mutate (from (g t c)) (to (g t t)) (rate s * pg0 * pt1 * pt2))
(mutate (from (t t c)) (to (t t a)) (rate n * pt0 * pt1 * pa2 * k))
(mutate (from (t t c)) (to (t a c)) (rate n * pt0 * pa1 * pc2 * k))
(mutate (from (t t c)) (to (t c c)) (rate n * pt0 * pc1 * pc2))
(mutate (from (t t c)) (to (t g c)) (rate n * pt0 * pg1 * pc2 * k))
(mutate (from (t t c)) (to (a t c)) (rate n * pa0 * pt1 * pc2 * k))
(mutate (from (t t c)) (to (c t c)) (rate n * pc0 * pt1 * pc2))
(mutate (from (t t c)) (to (g t c)) (rate n * pg0 * pt1 * pc2 * k))
(mutate (from (t t c)) (to (t t c)) (rate ~k * (const n) * ((const pa0) * (const pt1) * (const pc2) + (const pg0) * (const pt1) * (const pc2) + (const pt0) * (const pa1) * (const pc2) + (const pt0) * (const pg1) * (const pc2) + (const pt0) * (const pt1) * (const pa2) + (const pt0) * (const pt1) * (const pg2))))
(mutate (from (t t c)) (to (t t g)) (rate n * pt0 * pt1 * pg2 * k))
(mutate (from (t t c)) (to (t t t)) (rate s * pt0 * pt1 * pt2))
(mutate (from (a a g)) (to (a a a)) (rate s * pa0 * pa1 * pa2))
(mutate (from (a a g)) (to (a a c)) (rate n * pa0 * pa1 * pc2 * k))
(mutate (from (a a g)) (to (a a g)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pg2) + (const pa0) * (const pc1) * (const pg2) + (const pa0) * (const pt1) * (const pg2) + (const pa0) * (const pa1) * (const pc2) + (const pa0) * (const pa1) * (const pt2))))
(mutate (from (a a g)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (a a g)) (to (g a g)) (rate n * pg0 * pa1 * pg2))
(mutate (from (a a g)) (to (a c g)) (rate n * pa0 * pc1 * pg2 * k))
(mutate (from (a a g)) (to (a g g)) (rate n * pa0 * pg1 * pg2))
(mutate (from (a a g)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (a a g)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (c a g)) (to (c a a)) (rate s * pc0 * pa1 * pa2))
(mutate (from (c a g)) (to (c a c)) (rate n * pc0 * pa1 * pc2 * k))
(mutate (from (c a g)) (to (a a g)) (rate n * pa0 * pa1 * pg2 * k))
(mutate (from (c a g)) (to (c a g)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pg2) + (const pg0) * (const pa1) * (const pg2) + (const pc0) * (const pc1) * (const pg2) + (const pc0) * (const pt1) * (const pg2) + (const pc0) * (const pa1) * (const pc2) + (const pc0) * (const pa1) * (const pt2))))
(mutate (from (c a g)) (to (g a g)) (rate n * pg0 * pa1 * pg2 * k))
(mutate (from (c a g)) (to (c c g)) (rate n * pc0 * pc1 * pg2 * k))
(mutate (from (c a g)) (to (c g g)) (rate n * pc0 * pg1 * pg2))
(mutate (from (c a g)) (to (c t g)) (rate n * pc0 * pt1 * pg2 * k))
(mutate (from (c a g)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (g a g)) (to (g a a)) (rate s * pg0 * pa1 * pa2))
(mutate (from (g a g)) (to (g a c)) (rate n * pg0 * pa1 * pc2 * k))
(mutate (from (g a g)) (to (a a g)) (rate n * pa0 * pa1 * pg2))
(mutate (from (g a g)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (g a g)) (to (g a g)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pg2) + (const pg0) * (const pc1) * (const pg2) + (const pg0) * (const pt1) * (const pg2) + (const pg0) * (const pa1) * (const pc2) + (const pg0) * (const pa1) * (const pt2))))
(mutate (from (g a g)) (to (g c g)) (rate n * pg0 * pc1 * pg2 * k))
(mutate (from (g a g)) (to (g g g)) (rate n * pg0 * pg1 * pg2))
(mutate (from (g a g)) (to (g t g)) (rate n * pg0 * pt1 * pg2 * k))
(mutate (from (g a g)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (a c g)) (to (a c a)) (rate s * pa0 * pc1 * pa2))
(mutate (from (a c g)) (to (a c c)) (rate s * pa0 * pc1 * pc2 * k))
(mutate (from (a c g)) (to (a a g)) (rate n * pa0 * pa1 * pg2 * k))
(mutate (from (a c g)) (to (a c g)) (rate ~k * ((const s) * ((const pa0) * (const pc1) * (const pc2) + (const pa0) * (const pc1) * (const pt2)) + (const n) * ((const pc0) * (const pc1) * (const pg2) + (const pt0) * (const pc1) * (const pg2) + (const pa0) * (const pa1) * (const pg2) + (const pa0) * (const pg1) * (const pg2)))))
(mutate (from (a c g)) (to (c c g)) (rate n * pc0 * pc1 * pg2 * k))
(mutate (from (a c g)) (to (g c g)) (rate n * pg0 * pc1 * pg2))
(mutate (from (a c g)) (to (t c g)) (rate n * pt0 * pc1 * pg2 * k))
(mutate (from (a c g)) (to (a g g)) (rate n * pa0 * pg1 * pg2 * k))
(mutate (from (a c g)) (to (a t g)) (rate n * pa0 * pt1 * pg2))
(mutate (from (a c g)) (to (a c t)) (rate s * pa0 * pc1 * pt2 * k))
(mutate (from (c c g)) (to (c c a)) (rate s * pc0 * pc1 * pa2))
(mutate (from (c c g)) (to (c c c)) (rate s * pc0 * pc1 * pc2 * k))
(mutate (from (c c g)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (c c g)) (to (a c g)) (rate n * pa0 * pc1 * pg2 * k))
(mutate (from (c c g)) (to (c c g)) (rate ~k * ((const s) * ((const pc0) * (const pc1) * (const pc2) + (const pc0) * (const pc1) * (const pt2)) + (const n) * ((const pa0) * (const pc1) * (const pg2) + (const pg0) * (const pc1) * (const pg2) + (const pc0) * (const pa1) * (const pg2) + (const pc0) * (const pg1) * (const pg2)))))
(mutate (from (c c g)) (to (g c g)) (rate n * pg0 * pc1 * pg2 * k))
(mutate (from (c c g)) (to (t c g)) (rate n * pt0 * pc1 * pg2))
(mutate (from (c c g)) (to (c g g)) (rate n * pc0 * pg1 * pg2 * k))
(mutate (from (c c g)) (to (c t g)) (rate n * pc0 * pt1 * pg2))
(mutate (from (c c g)) (to (c c t)) (rate s * pc0 * pc1 * pt2 * k))
(mutate (from (g c g)) (to (g c a)) (rate s * pg0 * pc1 * pa2))
(mutate (from (g c g)) (to (g c c)) (rate s * pg0 * pc1 * pc2 * k))
(mutate (from (g c g)) (to (g a g)) (rate n * pg0 * pa1 * pg2 * k))
(mutate (from (g c g)) (to (a c g)) (rate n * pa0 * pc1 * pg2))
(mutate (from (g c g)) (to (c c g)) (rate n * pc0 * pc1 * pg2 * k))
(mutate (from (g c g)) (to (g c g)) (rate ~k * ((const s) * ((const pg0) * (const pc1) * (const pc2) + (const pg0) * (const pc1) * (const pt2)) + (const n) * ((const pc0) * (const pc1) * (const pg2) + (const pt0) * (const pc1) * (const pg2) + (const pg0) * (const pa1) * (const pg2) + (const pg0) * (const pg1) * (const pg2)))))
(mutate (from (g c g)) (to (t c g)) (rate n * pt0 * pc1 * pg2 * k))
(mutate (from (g c g)) (to (g g g)) (rate n * pg0 * pg1 * pg2 * k))
(mutate (from (g c g)) (to (g t g)) (rate n * pg0 * pt1 * pg2))
(mutate (from (g c g)) (to (g c t)) (rate s * pg0 * pc1 * pt2 * k))
(mutate (from (t c g)) (to (t c a)) (rate s * pt0 * pc1 * pa2))
(mutate (from (t c g)) (to (t c c)) (rate s * pt0 * pc1 * pc2 * k))
(mutate (from (t c g)) (to (a c g)) (rate n * pa0 * pc1 * pg2 * k))
(mutate (from (t c g)) (to (c c g)) (rate n * pc0 * pc1 * pg2))
(mutate (from (t c g)) (to (g c g)) (rate n * pg0 * pc1 * pg2 * k))
(mutate (from (t c g)) (to (t c g)) (rate ~k * ((const s) * ((const pt0) * (const pc1) * (const pc2) + (const pt0) * (const pc1) * (const pt2)) + (const n) * ((const pa0) * (const pc1) * (const pg2) + (const pg0) * (const pc1) * (const pg2) + (const pt0) * (const pg1) * (const pg2)))))
(mutate (from (t c g)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (t c g)) (to (t t g)) (rate n * pt0 * pt1 * pg2))
(mutate (from (t c g)) (to (t c t)) (rate s * pt0 * pc1 * pt2 * k))
(mutate (from (a g g)) (to (a g a)) (rate s * pa0 * pg1 * pa2))
(mutate (from (a g g)) (to (a g c)) (rate n * pa0 * pg1 * pc2 * k))
(mutate (from (a g g)) (to (a a g)) (rate n * pa0 * pa1 * pg2))
(mutate (from (a g g)) (to (a c g)) (rate n * pa0 * pc1 * pg2 * k))
(mutate (from (a g g)) (to (a g g)) (rate ~k * ((const s) * (const pc0) * (const pg1) * (const pg2) + (const n) * ((const pt0) * (const pg1) * (const pg2) + (const pa0) * (const pc1) * (const pg2) + (const pa0) * (const pt1) * (const pg2) + (const pa0) * (const pg1) * (const pc2) + (const pa0) * (const pg1) * (const pt2)))))
(mutate (from (a g g)) (to (c g g)) (rate s * pc0 * pg1 * pg2 * k))
(mutate (from (a g g)) (to (g g g)) (rate n * pg0 * pg1 * pg2))
(mutate (from (a g g)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (a g g)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (a g g)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (c g g)) (to (c g a)) (rate s * pc0 * pg1 * pa2))
(mutate (from (c g g)) (to (c g c)) (rate s * pc0 * pg1 * pc2 * k))
(mutate (from (c g g)) (to (c a g)) (rate n * pc0 * pa1 * pg2))
(mutate (from (c g g)) (to (c c g)) (rate n * pc0 * pc1 * pg2 * k))
(mutate (from (c g g)) (to (a g g)) (rate s * pa0 * pg1 * pg2 * k))
(mutate (from (c g g)) (to (c g g)) (rate ~k * ((const s) * ((const pa0) * (const pg1) * (const pg2) + (const pc0) * (const pg1) * (const pc2) + (const pc0) * (const pg1) * (const pt2)) + (const n) * ((const pg0) * (const pg1) * (const pg2) + (const pc0) * (const pc1) * (const pg2) + (const pc0) * (const pt1) * (const pg2)))))
(mutate (from (c g g)) (to (g g g)) (rate n * pg0 * pg1 * pg2 * k))
(mutate (from (c g g)) (to (t g g)) (rate n * pt0 * pg1 * pg2))
(mutate (from (c g g)) (to (c t g)) (rate n * pc0 * pt1 * pg2 * k))
(mutate (from (c g g)) (to (c g t)) (rate s * pc0 * pg1 * pt2 * k))
(mutate (from (g g g)) (to (g g a)) (rate s * pg0 * pg1 * pa2))
(mutate (from (g g g)) (to (g g c)) (rate s * pg0 * pg1 * pc2 * k))
(mutate (from (g g g)) (to (g a g)) (rate n * pg0 * pa1 * pg2))
(mutate (from (g g g)) (to (g c g)) (rate n * pg0 * pc1 * pg2 * k))
(mutate (from (g g g)) (to (a g g)) (rate n * pa0 * pg1 * pg2))
(mutate (from (g g g)) (to (c g g)) (rate n * pc0 * pg1 * pg2 * k))
(mutate (from (g g g)) (to (g g g)) (rate ~k * ((const s) * ((const pg0) * (const pg1) * (const pc2) + (const pg0) * (const pg1) * (const pt2)) + (const n) * ((const pc0) * (const pg1) * (const pg2) + (const pt0) * (const pg1) * (const pg2) + (const pg0) * (const pc1) * (const pg2) + (const pg0) * (const pt1) * (const pg2)))))
(mutate (from (g g g)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (g g g)) (to (g t g)) (rate n * pg0 * pt1 * pg2 * k))
(mutate (from (g g g)) (to (g g t)) (rate s * pg0 * pg1 * pt2 * k))
(mutate (from (t g g)) (to (t g c)) (rate n * pt0 * pg1 * pc2 * k))
(mutate (from (t g g)) (to (t c g)) (rate n * pt0 * pc1 * pg2 * k))
(mutate (from (t g g)) (to (a g g)) (rate n * pa0 * pg1 * pg2 * k))
(mutate (from (t g g)) (to (c g g)) (rate n * pc0 * pg1 * pg2))
(mutate (from (t g g)) (to (g g g)) (rate n * pg0 * pg1 * pg2 * k))
(mutate (from (t g g)) (to (t g g)) (rate ~k * (const n) * ((const pa0) * (const pg1) * (const pg2) + (const pg0) * (const pg1) * (const pg2) + (const pt0) * (const pc1) * (const pg2) + (const pt0) * (const pt1) * (const pg2) + (const pt0) * (const pg1) * (const pc2) + (const pt0) * (const pg1) * (const pt2))))
(mutate (from (t g g)) (to (t t g)) (rate n * pt0 * pt1 * pg2 * k))
(mutate (from (t g g)) (to (t g t)) (rate n * pt0 * pg1 * pt2 * k))
(mutate (from (a t g)) (to (a t a)) (rate n * pa0 * pt1 * pa2))
(mutate (from (a t g)) (to (a t c)) (rate n * pa0 * pt1 * pc2 * k))
(mutate (from (a t g)) (to (a a g)) (rate n * pa0 * pa1 * pg2 * k))
(mutate (from (a t g)) (to (a c g)) (rate n * pa0 * pc1 * pg2))
(mutate (from (a t g)) (to (a g g)) (rate n * pa0 * pg1 * pg2 * k))
(mutate (from (a t g)) (to (a t g)) (rate ~k * (const n) * ((const pc0) * (const pt1) * (const pg2) + (const pt0) * (const pt1) * (const pg2) + (const pa0) * (const pa1) * (const pg2) + (const pa0) * (const pg1) * (const pg2) + (const pa0) * (const pt1) * (const pc2) + (const pa0) * (const pt1) * (const pt2))))
(mutate (from (a t g)) (to (c t g)) (rate n * pc0 * pt1 * pg2 * k))
(mutate (from (a t g)) (to (g t g)) (rate n * pg0 * pt1 * pg2))
(mutate (from (a t g)) (to (t t g)) (rate n * pt0 * pt1 * pg2 * k))
(mutate (from (a t g)) (to (a t t)) (rate n * pa0 * pt1 * pt2 * k))
(mutate (from (c t g)) (to (c t a)) (rate s * pc0 * pt1 * pa2))
(mutate (from (c t g)) (to (c t c)) (rate s * pc0 * pt1 * pc2 * k))
(mutate (from (c t g)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (c t g)) (to (c c g)) (rate n * pc0 * pc1 * pg2))
(mutate (from (c t g)) (to (c g g)) (rate n * pc0 * pg1 * pg2 * k))
(mutate (from (c t g)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (c t g)) (to (c t g)) (rate ~k * ((const s) * ((const pc0) * (const pt1) * (const pc2) + (const pc0) * (const pt1) * (const pt2)) + (const n) * ((const pa0) * (const pt1) * (const pg2) + (const pg0) * (const pt1) * (const pg2) + (const pc0) * (const pa1) * (const pg2) + (const pc0) * (const pg1) * (const pg2)))))
(mutate (from (c t g)) (to (g t g)) (rate n * pg0 * pt1 * pg2 * k))
(mutate (from (c t g)) (to (t t g)) (rate s * pt0 * pt1 * pg2))
(mutate (from (c t g)) (to (c t t)) (rate s * pc0 * pt1 * pt2 * k))
(mutate (from (g t g)) (to (g t a)) (rate s * pg0 * pt1 * pa2))
(mutate (from (g t g)) (to (g t c)) (rate s * pg0 * pt1 * pc2 * k))
(mutate (from (g t g)) (to (g a g)) (rate n * pg0 * pa1 * pg2 * k))
(mutate (from (g t g)) (to (g c g)) (rate n * pg0 * pc1 * pg2))
(mutate (from (g t g)) (to (g g g)) (rate n * pg0 * pg1 * pg2 * k))
(mutate (from (g t g)) (to (a t g)) (rate n * pa0 * pt1 * pg2))
(mutate (from (g t g)) (to (c t g)) (rate n * pc0 * pt1 * pg2 * k))
(mutate (from (g t g)) (to (g t g)) (rate ~k * ((const s) * ((const pg0) * (const pt1) * (const pc2) + (const pg0) * (const pt1) * (const pt2)) + (const n) * ((const pc0) * (const pt1) * (const pg2) + (const pt0) * (const pt1) * (const pg2) + (const pg0) * (const pa1) * (const pg2) + (const pg0) * (const pg1) * (const pg2)))))
(mutate (from (g t g)) (to (t t g)) (rate n * pt0 * pt1 * pg2 * k))
(mutate (from (g t g)) (to (g t t)) (rate s * pg0 * pt1 * pt2 * k))
(mutate (from (t t g)) (to (t t a)) (rate s * pt0 * pt1 * pa2))
(mutate (from (t t g)) (to (t t c)) (rate n * pt0 * pt1 * pc2 * k))
(mutate (from (t t g)) (to (t c g)) (rate n * pt0 * pc1 * pg2))
(mutate (from (t t g)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (t t g)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (t t g)) (to (c t g)) (rate s * pc0 * pt1 * pg2))
(mutate (from (t t g)) (to (g t g)) (rate n * pg0 * pt1 * pg2 * k))
(mutate (from (t t g)) (to (t t g)) (rate ~k * (const n) * ((const pa0) * (const pt1) * (const pg2) + (const pg0) * (const pt1) * (const pg2) + (const pt0) * (const pg1) * (const pg2) + (const pt0) * (const pt1) * (const pc2) + (const pt0) * (const pt1) * (const pt2))))
(mutate (from (t t g)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (a a t)) (to (a a a)) (rate n * pa0 * pa1 * pa2 * k))
(mutate (from (a a t)) (to (a a c)) (rate s * pa0 * pa1 * pc2))
(mutate (from (a a t)) (to (a a g)) (rate n * pa0 * pa1 * pg2 * k))
(mutate (from (a a t)) (to (a a t)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pt2) + (const pt0) * (const pa1) * (const pt2) + (const pa0) * (const pc1) * (const pt2) + (const pa0) * (const pt1) * (const pt2) + (const pa0) * (const pa1) * (const pa2) + (const pa0) * (const pa1) * (const pg2))))
(mutate (from (a a t)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (a a t)) (to (g a t)) (rate n * pg0 * pa1 * pt2))
(mutate (from (a a t)) (to (t a t)) (rate n * pt0 * pa1 * pt2 * k))
(mutate (from (a a t)) (to (a c t)) (rate n * pa0 * pc1 * pt2 * k))
(mutate (from (a a t)) (to (a g t)) (rate n * pa0 * pg1 * pt2))
(mutate (from (a a t)) (to (a t t)) (rate n * pa0 * pt1 * pt2 * k))
(mutate (from (c a t)) (to (c a a)) (rate n * pc0 * pa1 * pa2 * k))
(mutate (from (c a t)) (to (c a c)) (rate s * pc0 * pa1 * pc2))
(mutate (from (c a t)) (to (c a g)) (rate n * pc0 * pa1 * pg2 * k))
(mutate (from (c a t)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (c a t)) (to (c a t)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pt2) + (const pg0) * (const pa1) * (const pt2) + (const pc0) * (const pc1) * (const pt2) + (const pc0) * (const pt1) * (const pt2) + (const pc0) * (const pa1) * (const pa2) + (const pc0) * (const pa1) * (const pg2))))
(mutate (from (c a t)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (c a t)) (to (t a t)) (rate n * pt0 * pa1 * pt2))
(mutate (from (c a t)) (to (c c t)) (rate n * pc0 * pc1 * pt2 * k))
(mutate (from (c a t)) (to (c g t)) (rate n * pc0 * pg1 * pt2))
(mutate (from (c a t)) (to (c t t)) (rate n * pc0 * pt1 * pt2 * k))
(mutate (from (g a t)) (to (g a a)) (rate n * pg0 * pa1 * pa2 * k))
(mutate (from (g a t)) (to (g a c)) (rate s * pg0 * pa1 * pc2))
(mutate (from (g a t)) (to (g a g)) (rate n * pg0 * pa1 * pg2 * k))
(mutate (from (g a t)) (to (a a t)) (rate n * pa0 * pa1 * pt2))
(mutate (from (g a t)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (g a t)) (to (g a t)) (rate ~k * (const n) * ((const pc0) * (const pa1) * (const pt2) + (const pt0) * (const pa1) * (const pt2) + (const pg0) * (const pc1) * (const pt2) + (const pg0) * (const pt1) * (const pt2) + (const pg0) * (const pa1) * (const pa2) + (const pg0) * (const pa1) * (const pg2))))
(mutate (from (g a t)) (to (t a t)) (rate n * pt0 * pa1 * pt2 * k))
(mutate (from (g a t)) (to (g c t)) (rate n * pg0 * pc1 * pt2 * k))
(mutate (from (g a t)) (to (g g t)) (rate n * pg0 * pg1 * pt2))
(mutate (from (g a t)) (to (g t t)) (rate n * pg0 * pt1 * pt2 * k))
(mutate (from (t a t)) (to (t a c)) (rate s * pt0 * pa1 * pc2))
(mutate (from (t a t)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (t a t)) (to (c a t)) (rate n * pc0 * pa1 * pt2))
(mutate (from (t a t)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (t a t)) (to (t a t)) (rate ~k * (const n) * ((const pa0) * (const pa1) * (const pt2) + (const pg0) * (const pa1) * (const pt2) + (const pt0) * (const pc1) * (const pt2) + (const pt0) * (const pt1) * (const pt2))))
(mutate (from (t a t)) (to (t c t)) (rate n * pt0 * pc1 * pt2 * k))
(mutate (from (t a t)) (to (t g t)) (rate n * pt0 * pg1 * pt2))
(mutate (from (t a t)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (a c t)) (to (a c a)) (rate s * pa0 * pc1 * pa2 * k))
(mutate (from (a c t)) (to (a c c)) (rate s * pa0 * pc1 * pc2))
(mutate (from (a c t)) (to (a c g)) (rate s * pa0 * pc1 * pg2 * k))
(mutate (from (a c t)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (a c t)) (to (a c t)) (rate ~k * ((const s) * ((const pa0) * (const pc1) * (const pa2) + (const pa0) * (const pc1) * (const pg2)) + (const n) * ((const pc0) * (const pc1) * (const pt2) + (const pt0) * (const pc1) * (const pt2) + (const pa0) * (const pa1) * (const pt2) + (const pa0) * (const pg1) * (const pt2)))))
(mutate (from (a c t)) (to (c c t)) (rate n * pc0 * pc1 * pt2 * k))
(mutate (from (a c t)) (to (g c t)) (rate n * pg0 * pc1 * pt2))
(mutate (from (a c t)) (to (t c t)) (rate n * pt0 * pc1 * pt2 * k))
(mutate (from (a c t)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (a c t)) (to (a t t)) (rate n * pa0 * pt1 * pt2))
(mutate (from (c c t)) (to (c c a)) (rate s * pc0 * pc1 * pa2 * k))
(mutate (from (c c t)) (to (c c c)) (rate s * pc0 * pc1 * pc2))
(mutate (from (c c t)) (to (c c g)) (rate s * pc0 * pc1 * pg2 * k))
(mutate (from (c c t)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (c c t)) (to (a c t)) (rate n * pa0 * pc1 * pt2 * k))
(mutate (from (c c t)) (to (c c t)) (rate ~k * ((const s) * ((const pc0) * (const pc1) * (const pa2) + (const pc0) * (const pc1) * (const pg2)) + (const n) * ((const pa0) * (const pc1) * (const pt2) + (const pg0) * (const pc1) * (const pt2) + (const pc0) * (const pa1) * (const pt2) + (const pc0) * (const pg1) * (const pt2)))))
(mutate (from (c c t)) (to (g c t)) (rate n * pg0 * pc1 * pt2 * k))
(mutate (from (c c t)) (to (t c t)) (rate n * pt0 * pc1 * pt2))
(mutate (from (c c t)) (to (c g t)) (rate n * pc0 * pg1 * pt2 * k))
(mutate (from (c c t)) (to (c t t)) (rate n * pc0 * pt1 * pt2))
(mutate (from (g c t)) (to (g c a)) (rate s * pg0 * pc1 * pa2 * k))
(mutate (from (g c t)) (to (g c c)) (rate s * pg0 * pc1 * pc2))
(mutate (from (g c t)) (to (g c g)) (rate s * pg0 * pc1 * pg2 * k))
(mutate (from (g c t)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (g c t)) (to (a c t)) (rate n * pa0 * pc1 * pt2))
(mutate (from (g c t)) (to (c c t)) (rate n * pc0 * pc1 * pt2 * k))
(mutate (from (g c t)) (to (g c t)) (rate ~k * ((const s) * ((const pg0) * (const pc1) * (const pa2) + (const pg0) * (const pc1) * (const pg2)) + (const n) * ((const pc0) * (const pc1) * (const pt2) + (const pt0) * (const pc1) * (const pt2) + (const pg0) * (const pa1) * (const pt2) + (const pg0) * (const pg1) * (const pt2)))))
(mutate (from (g c t)) (to (t c t)) (rate n * pt0 * pc1 * pt2 * k))
(mutate (from (g c t)) (to (g g t)) (rate n * pg0 * pg1 * pt2 * k))
(mutate (from (g c t)) (to (g t t)) (rate n * pg0 * pt1 * pt2))
(mutate (from (t c t)) (to (t c a)) (rate s * pt0 * pc1 * pa2 * k))
(mutate (from (t c t)) (to (t c c)) (rate s * pt0 * pc1 * pc2))
(mutate (from (t c t)) (to (t c g)) (rate s * pt0 * pc1 * pg2 * k))
(mutate (from (t c t)) (to (t a t)) (rate n * pt0 * pa1 * pt2 * k))
(mutate (from (t c t)) (to (a c t)) (rate n * pa0 * pc1 * pt2 * k))
(mutate (from (t c t)) (to (c c t)) (rate n * pc0 * pc1 * pt2))
(mutate (from (t c t)) (to (g c t)) (rate n * pg0 * pc1 * pt2 * k))
(mutate (from (t c t)) (to (t c t)) (rate ~k * ((const s) * ((const pt0) * (const pc1) * (const pa2) + (const pt0) * (const pc1) * (const pg2)) + (const n) * ((const pa0) * (const pc1) * (const pt2) + (const pg0) * (const pc1) * (const pt2) + (const pt0) * (const pa1) * (const pt2) + (const pt0) * (const pg1) * (const pt2)))))
(mutate (from (t c t)) (to (t g t)) (rate n * pt0 * pg1 * pt2 * k))
(mutate (from (t c t)) (to (t t t)) (rate n * pt0 * pt1 * pt2))
(mutate (from (a g t)) (to (a g a)) (rate n * pa0 * pg1 * pa2 * k))
(mutate (from (a g t)) (to (a g c)) (rate s * pa0 * pg1 * pc2))
(mutate (from (a g t)) (to (a g g)) (rate n * pa0 * pg1 * pg2 * k))
(mutate (from (a g t)) (to (a a t)) (rate n * pa0 * pa1 * pt2))
(mutate (from (a g t)) (to (a c t)) (rate n * pa0 * pc1 * pt2 * k))
(mutate (from (a g t)) (to (a g t)) (rate ~k * (const n) * ((const pc0) * (const pg1) * (const pt2) + (const pt0) * (const pg1) * (const pt2) + (const pa0) * (const pc1) * (const pt2) + (const pa0) * (const pt1) * (const pt2) + (const pa0) * (const pg1) * (const pa2) + (const pa0) * (const pg1) * (const pg2))))
(mutate (from (a g t)) (to (c g t)) (rate n * pc0 * pg1 * pt2 * k))
(mutate (from (a g t)) (to (g g t)) (rate n * pg0 * pg1 * pt2))
(mutate (from (a g t)) (to (t g t)) (rate n * pt0 * pg1 * pt2 * k))
(mutate (from (a g t)) (to (a t t)) (rate n * pa0 * pt1 * pt2 * k))
(mutate (from (c g t)) (to (c g a)) (rate s * pc0 * pg1 * pa2 * k))
(mutate (from (c g t)) (to (c g c)) (rate s * pc0 * pg1 * pc2))
(mutate (from (c g t)) (to (c g g)) (rate s * pc0 * pg1 * pg2 * k))
(mutate (from (c g t)) (to (c a t)) (rate n * pc0 * pa1 * pt2))
(mutate (from (c g t)) (to (c c t)) (rate n * pc0 * pc1 * pt2 * k))
(mutate (from (c g t)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (c g t)) (to (c g t)) (rate ~k * ((const s) * ((const pc0) * (const pg1) * (const pa2) + (const pc0) * (const pg1) * (const pg2)) + (const n) * ((const pa0) * (const pg1) * (const pt2) + (const pg0) * (const pg1) * (const pt2) + (const pc0) * (const pc1) * (const pt2) + (const pc0) * (const pt1) * (const pt2)))))
(mutate (from (c g t)) (to (g g t)) (rate n * pg0 * pg1 * pt2 * k))
(mutate (from (c g t)) (to (t g t)) (rate n * pt0 * pg1 * pt2))
(mutate (from (c g t)) (to (c t t)) (rate n * pc0 * pt1 * pt2 * k))
(mutate (from (g g t)) (to (g g a)) (rate s * pg0 * pg1 * pa2 * k))
(mutate (from (g g t)) (to (g g c)) (rate s * pg0 * pg1 * pc2))
(mutate (from (g g t)) (to (g g g)) (rate s * pg0 * pg1 * pg2 * k))
(mutate (from (g g t)) (to (g a t)) (rate n * pg0 * pa1 * pt2))
(mutate (from (g g t)) (to (g c t)) (rate n * pg0 * pc1 * pt2 * k))
(mutate (from (g g t)) (to (a g t)) (rate n * pa0 * pg1 * pt2))
(mutate (from (g g t)) (to (c g t)) (rate n * pc0 * pg1 * pt2 * k))
(mutate (from (g g t)) (to (g g t)) (rate ~k * ((const s) * ((const pg0) * (const pg1) * (const pa2) + (const pg0) * (const pg1) * (const pg2)) + (const n) * ((const pc0) * (const pg1) * (const pt2) + (const pt0) * (const pg1) * (const pt2) + (const pg0) * (const pc1) * (const pt2) + (const pg0) * (const pt1) * (const pt2)))))
(mutate (from (g g t)) (to (t g t)) (rate n * pt0 * pg1 * pt2 * k))
(mutate (from (g g t)) (to (g t t)) (rate n * pg0 * pt1 * pt2 * k))
(mutate (from (t g t)) (to (t g c)) (rate s * pt0 * pg1 * pc2))
(mutate (from (t g t)) (to (t g g)) (rate n * pt0 * pg1 * pg2 * k))
(mutate (from (t g t)) (to (t a t)) (rate n * pt0 * pa1 * pt2))
(mutate (from (t g t)) (to (t c t)) (rate n * pt0 * pc1 * pt2 * k))
(mutate (from (t g t)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (t g t)) (to (c g t)) (rate n * pc0 * pg1 * pt2))
(mutate (from (t g t)) (to (g g t)) (rate n * pg0 * pg1 * pt2 * k))
(mutate (from (t g t)) (to (t g t)) (rate ~k * (const n) * ((const pa0) * (const pg1) * (const pt2) + (const pg0) * (const pg1) * (const pt2) + (const pt0) * (const pc1) * (const pt2) + (const pt0) * (const pt1) * (const pt2) + (const pt0) * (const pg1) * (const pg2))))
(mutate (from (t g t)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (a t t)) (to (a t a)) (rate s * pa0 * pt1 * pa2 * k))
(mutate (from (a t t)) (to (a t c)) (rate s * pa0 * pt1 * pc2))
(mutate (from (a t t)) (to (a t g)) (rate n * pa0 * pt1 * pg2 * k))
(mutate (from (a t t)) (to (a a t)) (rate n * pa0 * pa1 * pt2 * k))
(mutate (from (a t t)) (to (a c t)) (rate n * pa0 * pc1 * pt2))
(mutate (from (a t t)) (to (a g t)) (rate n * pa0 * pg1 * pt2 * k))
(mutate (from (a t t)) (to (a t t)) (rate ~k * ((const s) * (const pa0) * (const pt1) * (const pa2) + (const n) * ((const pc0) * (const pt1) * (const pt2) + (const pt0) * (const pt1) * (const pt2) + (const pa0) * (const pa1) * (const pt2) + (const pa0) * (const pg1) * (const pt2) + (const pa0) * (const pt1) * (const pg2)))))
(mutate (from (a t t)) (to (c t t)) (rate n * pc0 * pt1 * pt2 * k))
(mutate (from (a t t)) (to (g t t)) (rate n * pg0 * pt1 * pt2))
(mutate (from (a t t)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (c t t)) (to (c t a)) (rate s * pc0 * pt1 * pa2 * k))
(mutate (from (c t t)) (to (c t c)) (rate s * pc0 * pt1 * pc2))
(mutate (from (c t t)) (to (c t g)) (rate s * pc0 * pt1 * pg2 * k))
(mutate (from (c t t)) (to (c a t)) (rate n * pc0 * pa1 * pt2 * k))
(mutate (from (c t t)) (to (c c t)) (rate n * pc0 * pc1 * pt2))
(mutate (from (c t t)) (to (c g t)) (rate n * pc0 * pg1 * pt2 * k))
(mutate (from (c t t)) (to (a t t)) (rate n * pa0 * pt1 * pt2 * k))
(mutate (from (c t t)) (to (c t t)) (rate ~k * ((const s) * ((const pc0) * (const pt1) * (const pa2) + (const pc0) * (const pt1) * (const pg2)) + (const n) * ((const pa0) * (const pt1) * (const pt2) + (const pg0) * (const pt1) * (const pt2) + (const pc0) * (const pa1) * (const pt2) + (const pc0) * (const pg1) * (const pt2)))))
(mutate (from (c t t)) (to (g t t)) (rate n * pg0 * pt1 * pt2 * k))
(mutate (from (c t t)) (to (t t t)) (rate n * pt0 * pt1 * pt2))
(mutate (from (g t t)) (to (g t a)) (rate s * pg0 * pt1 * pa2 * k))
(mutate (from (g t t)) (to (g t c)) (rate s * pg0 * pt1 * pc2))
(mutate (from (g t t)) (to (g t g)) (rate s * pg0 * pt1 * pg2 * k))
(mutate (from (g t t)) (to (g a t)) (rate n * pg0 * pa1 * pt2 * k))
(mutate (from (g t t)) (to (g c t)) (rate n * pg0 * pc1 * pt2))
(mutate (from (g t t)) (to (g g t)) (rate n * pg0 * pg1 * pt2 * k))
(mutate (from (g t t)) (to (a t t)) (rate n * pa0 * pt1 * pt2))
(mutate (from (g t t)) (to (c t t)) (rate n * pc0 * pt1 * pt2 * k))
(mutate (from (g t t)) (to (g t t)) (rate ~k * ((const s) * ((const pg0) * (const pt1) * (const pa2) + (const pg0) * (const pt1) * (const pg2)) + (const n) * ((const pc0) * (const pt1) * (const pt2) + (const pt0) * (const pt1) * (const pt2) + (const pg0) * (const pa1) * (const pt2) + (const pg0) * (const pg1) * (const pt2)))))
(mutate (from (g t t)) (to (t t t)) (rate n * pt0 * pt1 * pt2 * k))
(mutate (from (t t t)) (to (t t a)) (rate n * pt0 * pt1 * pa2 * k))
(mutate (from (t t t)) (to (t t c)) (rate s * pt0 * pt1 * pc2))
(mutate (from (t t t)) (to (t t g)) (rate n * pt0 * pt1 * pg2 * k))
(mutate (from (t t t)) (to (t a t)) (rate n * pt0 * pa1 * pt2 * k))
(mutate (from (t t t)) (to (t c t)) (rate n * pt0 * pc1 * pt2))
(mutate (from (t t t)) (to (t g t)) (rate n * pt0 * pg1 * pt2 * k))
(mutate (from (t t t)) (to (a t t)) (rate n * pa0 * pt1 * pt2 * k))
(mutate (from (t t t)) (to (c t t)) (rate n * pc0 * pt1 * pt2))
(mutate (from (t t t)) (to (g t t)) (rate n * pg0 * pt1 * pt2 * k))
(mutate (from (t t t)) (to (t t t)) (rate ~k * (const n) * ((const pa0) * (const pt1) * (const pt2) + (const pg0) * (const pt1) * (const pt2) + (const pt0) * (const pa1) * (const pt2) + (const pt0) * (const pg1) * (const pt2) + (const pt0) * (const pt1) * (const pa2) + (const pt0) * (const pt1) * (const pg2))))
) ;; end hybrid chain COD0 COD1 COD2
) ;; end grammar CodeML_sn_f4x3
;; Alphabet DNA
;;
(alphabet
(name DNA)
(token (a c g t))
(complement (t g c a))
(extend (to n) (from a) (from c) (from g) (from t))
(extend (to x) (from a) (from c) (from g) (from t))
(extend (to u) (from t))
(extend (to r) (from a) (from g))
(extend (to y) (from c) (from t))
(extend (to m) (from a) (from c))
(extend (to k) (from g) (from t))
(extend (to s) (from c) (from g))
(extend (to w) (from a) (from t))
(extend (to h) (from a) (from c) (from t))
(extend (to b) (from c) (from g) (from t))
(extend (to v) (from a) (from c) (from g))
(extend (to d) (from a) (from g) (from t))
(wildcard *)
) ;; end alphabet DNA