;; Grammar pfold
;;
(grammar
 (name pfold)
 (update-rates 1)
 (update-rules 1)

 ;; Transformation rules for grammar symbols

 ;; State pfoldS
 ;;
 (transform (from (pfoldS)) (to (pfoldL)) (prob 0.0888798))
 (transform (from (pfoldS)) (to (pfoldB)) (prob 0.911301))

 ;; State pfoldF
 ;;
 (transform (from (pfoldF)) (to (LNUC pfoldF* RNUC)) (gaps-ok)
  (annotate (row SS_cons) (column LNUC) (label <))
  (annotate (row SS_cons) (column RNUC) (label >))
  (minlen 2))
 (transform (from (pfoldF*)) (to (pfoldF)) (prob 0.753667))
 (transform (from (pfoldF*)) (to (pfoldB)) (prob 0.2469))

 ;; State pfoldL
 ;;
 (transform (from (pfoldL)) (to (pfoldF)) (prob 0.0745835))
 (transform (from (pfoldL)) (to (pfoldU)) (prob 0.925946))

 ;; State pfoldB
 ;;
 (transform (from (pfoldB)) (to (pfoldL pfoldS)))

 ;; State pfoldU
 ;;
 (transform (from (pfoldU)) (to (NUC pfoldU*)) (gaps-ok)
  (annotate (row SS_cons) (column NUC) (label _))
  (minlen 1))
 (transform (from (pfoldU*)) (to ()) (prob 1))

 ;; Markov chain substitution models

 (chain
  (update-policy rev)
  (terminal (LNUC RNUC))

  ;; initial probability distribution
  (initial (state (a a)) (prob 0.0228465))
  (initial (state (c a)) (prob 0.0161447))
  (initial (state (g a)) (prob 0.0218842))
  (initial (state (u a)) (prob 0.164218))
  (initial (state (a c)) (prob 0.0121978))
  (initial (state (c c)) (prob 0.0110829))
  (initial (state (g c)) (prob 0.22142))
  (initial (state (u c)) (prob 0.00988232))
  (initial (state (a g)) (prob 0.0142639))
  (initial (state (c g)) (prob 0.216563))
  (initial (state (g g)) (prob 0.014943))
  (initial (state (u g)) (prob 0.0600486))
  (initial (state (a u)) (prob 0.135061))
  (initial (state (c u)) (prob 0.0105746))
  (initial (state (g u)) (prob 0.0487416))
  (initial (state (u u)) (prob 0.0201287))

  ;; mutation rates
  (mutate (from (a a)) (to (c a)) (rate 0.232935))
  (mutate (from (a a)) (to (g a)) (rate 0.278363))
  (mutate (from (a a)) (to (u a)) (rate 0.442669))
  (mutate (from (a a)) (to (a c)) (rate 0.21661))
  (mutate (from (a a)) (to (c c)) (rate 0.0163224))
  (mutate (from (a a)) (to (g c)) (rate 0.00529501))
  (mutate (from (a a)) (to (u c)) (rate 0.0451581))
  (mutate (from (a a)) (to (a g)) (rate 0.289094))
  (mutate (from (a a)) (to (c g)) (rate 0.00486023))
  (mutate (from (a a)) (to (g g)) (rate 0.0357234))
  (mutate (from (a a)) (to (u g)) (rate 0.0467622))
  (mutate (from (a a)) (to (a u)) (rate 0.417535))
  (mutate (from (a a)) (to (c u)) (rate 0.0574855))
  (mutate (from (a a)) (to (g u)) (rate 0.0657536))
  (mutate (from (a a)) (to (u u)) (rate 0.126285))
  (mutate (from (c a)) (to (a a)) (rate 0.329627))
  (mutate (from (c a)) (to (g a)) (rate 0.198078))
  (mutate (from (c a)) (to (u a)) (rate 1.05653))
  (mutate (from (c a)) (to (a c)) (rate 0.0443118))
  (mutate (from (c a)) (to (c c)) (rate 0.294163))
  (mutate (from (c a)) (to (g c)) (rate 0.00956298))
  (mutate (from (c a)) (to (u c)) (rate 0.0715911))
  (mutate (from (c a)) (to (a g)) (rate 0.0491335))
  (mutate (from (c a)) (to (c g)) (rate 0.944452))
  (mutate (from (c a)) (to (g g)) (rate 0.0298297))
  (mutate (from (c a)) (to (u g)) (rate 0.139075))
  (mutate (from (c a)) (to (a u)) (rate 0.0279239))
  (mutate (from (c a)) (to (c u)) (rate 0.418415))
  (mutate (from (c a)) (to (g u)) (rate 0.0309747))
  (mutate (from (c a)) (to (u u)) (rate 0.0807136))
  (mutate (from (g a)) (to (a a)) (rate 0.290603))
  (mutate (from (g a)) (to (c a)) (rate 0.146129))
  (mutate (from (g a)) (to (u a)) (rate 0.20632))
  (mutate (from (g a)) (to (a c)) (rate 0.0150121))
  (mutate (from (g a)) (to (c c)) (rate 0.0138578))
  (mutate (from (g a)) (to (g c)) (rate 0.17892))
  (mutate (from (g a)) (to (u c)) (rate 0.0285063))
  (mutate (from (g a)) (to (a g)) (rate 0.041656))
  (mutate (from (g a)) (to (c g)) (rate 0.0112407))
  (mutate (from (g a)) (to (g g)) (rate 0.399829))
  (mutate (from (g a)) (to (u g)) (rate 0.0159419))
  (mutate (from (g a)) (to (a u)) (rate 0.0600181))
  (mutate (from (g a)) (to (c u)) (rate 0.0142424))
  (mutate (from (g a)) (to (g u)) (rate 0.206404))
  (mutate (from (g a)) (to (u u)) (rate 0.0733953))
  (mutate (from (u a)) (to (a a)) (rate 0.0615855))
  (mutate (from (u a)) (to (c a)) (rate 0.103871))
  (mutate (from (u a)) (to (g a)) (rate 0.0274949))
  (mutate (from (u a)) (to (a c)) (rate 0.00572901))
  (mutate (from (u a)) (to (c c)) (rate 0.000302498))
  (mutate (from (u a)) (to (g c)) (rate 0.125656))
  (mutate (from (u a)) (to (u c)) (rate 0.0435469))
  (mutate (from (u a)) (to (a g)) (rate 0.0117235))
  (mutate (from (u a)) (to (c g)) (rate 0.392175))
  (mutate (from (u a)) (to (g g)) (rate 0.00346473))
  (mutate (from (u a)) (to (u g)) (rate 0.20071))
  (mutate (from (u a)) (to (a u)) (rate 0.186955))
  (mutate (from (u a)) (to (c u)) (rate 0.00182837))
  (mutate (from (u a)) (to (g u)) (rate 0.0225739))
  (mutate (from (u a)) (to (u u)) (rate 0.0810523))
  (mutate (from (a c)) (to (a a)) (rate 0.405709))
  (mutate (from (a c)) (to (c a)) (rate 0.0586499))
  (mutate (from (a c)) (to (g a)) (rate 0.0269333))
  (mutate (from (a c)) (to (u a)) (rate 0.0771289))
  (mutate (from (a c)) (to (c c)) (rate 0.319768))
  (mutate (from (a c)) (to (g c)) (rate 0.859852))
  (mutate (from (a c)) (to (u c)) (rate 0.34587))
  (mutate (from (a c)) (to (a g)) (rate 0.146981))
  (mutate (from (a c)) (to (c g)) (rate 0.0319116))
  (mutate (from (a c)) (to (g g)) (rate 0.120589))
  (mutate (from (a c)) (to (u g)) (rate 0.0406886))
  (mutate (from (a c)) (to (a u)) (rate 0.814662))
  (mutate (from (a c)) (to (c u)) (rate 0.0384822))
  (mutate (from (a c)) (to (g u)) (rate 0.35091))
  (mutate (from (a c)) (to (u u)) (rate 0.234822))
  (mutate (from (c c)) (to (a a)) (rate 0.0336472))
  (mutate (from (c c)) (to (c a)) (rate 0.428515))
  (mutate (from (c c)) (to (g a)) (rate 0.0273636))
  (mutate (from (c c)) (to (u a)) (rate 0.0044822))
  (mutate (from (c c)) (to (a c)) (rate 0.351938))
  (mutate (from (c c)) (to (g c)) (rate 0.341469))
  (mutate (from (c c)) (to (u c)) (rate 0.910666))
  (mutate (from (c c)) (to (a g)) (rate 0.0115937))
  (mutate (from (c c)) (to (c g)) (rate 0.502437))
  (mutate (from (c c)) (to (g g)) (rate 0.0298207))
  (mutate (from (c c)) (to (u g)) (rate 0.053901))
  (mutate (from (c c)) (to (a u)) (rate 0.00164932))
  (mutate (from (c c)) (to (c u)) (rate 0.843265))
  (mutate (from (c c)) (to (g u)) (rate 0.0430873))
  (mutate (from (c c)) (to (u u)) (rate 0.0620845))
  (mutate (from (g c)) (to (a a)) (rate 0.000546348))
  (mutate (from (g c)) (to (c a)) (rate 0.00069728))
  (mutate (from (g c)) (to (g a)) (rate 0.0176837))
  (mutate (from (g c)) (to (u a)) (rate 0.0931936))
  (mutate (from (g c)) (to (a c)) (rate 0.0473685))
  (mutate (from (g c)) (to (c c)) (rate 0.0170918))
  (mutate (from (g c)) (to (u c)) (rate 0.0220961))
  (mutate (from (g c)) (to (a g)) (rate 0.00220435))
  (mutate (from (g c)) (to (c g)) (rate 0.138649))
  (mutate (from (g c)) (to (g g)) (rate 0.0212823))
  (mutate (from (g c)) (to (u g)) (rate 0.0171876))
  (mutate (from (g c)) (to (a u)) (rate 0.284742))
  (mutate (from (g c)) (to (c u)) (rate 0.00310648))
  (mutate (from (g c)) (to (g u)) (rate 0.183016))
  (mutate (from (g c)) (to (u u)) (rate 0.0072272))
  (mutate (from (u c)) (to (a a)) (rate 0.104399))
  (mutate (from (u c)) (to (c a)) (rate 0.116958))
  (mutate (from (u c)) (to (g a)) (rate 0.0631267))
  (mutate (from (u c)) (to (u a)) (rate 0.723633))
  (mutate (from (u c)) (to (a c)) (rate 0.42691))
  (mutate (from (u c)) (to (c c)) (rate 1.0213))
  (mutate (from (u c)) (to (g c)) (rate 0.495077))
  (mutate (from (u c)) (to (a g)) (rate 0.0772664))
  (mutate (from (u c)) (to (c g)) (rate 0.0997815))
  (mutate (from (u c)) (to (g g)) (rate 0.21653))
  (mutate (from (u c)) (to (u g)) (rate 0.396524))
  (mutate (from (u c)) (to (a u)) (rate 0.151578))
  (mutate (from (u c)) (to (c u)) (rate 0.327868))
  (mutate (from (u c)) (to (g u)) (rate 0.0655005))
  (mutate (from (u c)) (to (u u)) (rate 0.969586))
  (mutate (from (a g)) (to (a a)) (rate 0.463042))
  (mutate (from (a g)) (to (c a)) (rate 0.0556122))
  (mutate (from (a g)) (to (g a)) (rate 0.0639101))
  (mutate (from (a g)) (to (u a)) (rate 0.134971))
  (mutate (from (a g)) (to (a c)) (rate 0.125691))
  (mutate (from (a g)) (to (c c)) (rate 0.00900819))
  (mutate (from (a g)) (to (g c)) (rate 0.0342183))
  (mutate (from (a g)) (to (u c)) (rate 0.0535317))
  (mutate (from (a g)) (to (c g)) (rate 0.37781))
  (mutate (from (a g)) (to (g g)) (rate 0.381481))
  (mutate (from (a g)) (to (u g)) (rate 0.2406))
  (mutate (from (a g)) (to (a u)) (rate 0.377184))
  (mutate (from (a g)) (to (c u)) (rate 0.0457857))
  (mutate (from (a g)) (to (g u)) (rate 0.0672571))
  (mutate (from (a g)) (to (u u)) (rate 0.156892))
  (mutate (from (c g)) (to (a a)) (rate 0.000512734))
  (mutate (from (c g)) (to (c a)) (rate 0.0704088))
  (mutate (from (c g)) (to (g a)) (rate 0.0011359))
  (mutate (from (c g)) (to (u a)) (rate 0.297384))
  (mutate (from (c g)) (to (a c)) (rate 0.00179741))
  (mutate (from (c g)) (to (c c)) (rate 0.0257129))
  (mutate (from (c g)) (to (g c)) (rate 0.141759))
  (mutate (from (c g)) (to (u c)) (rate 0.00455329))
  (mutate (from (c g)) (to (a g)) (rate 0.0248845))
  (mutate (from (c g)) (to (g g)) (rate 0.0279372))
  (mutate (from (c g)) (to (u g)) (rate 0.172287))
  (mutate (from (c g)) (to (a u)) (rate 0.109935))
  (mutate (from (c g)) (to (c u)) (rate 0.024824))
  (mutate (from (c g)) (to (g u)) (rate 0.0296638))
  (mutate (from (c g)) (to (u u)) (rate 0.0111359))
  (mutate (from (g g)) (to (a a)) (rate 0.0546176))
  (mutate (from (g g)) (to (c a)) (rate 0.0322285))
  (mutate (from (g g)) (to (g a)) (rate 0.585553))
  (mutate (from (g g)) (to (u a)) (rate 0.0380759))
  (mutate (from (g g)) (to (a c)) (rate 0.0984358))
  (mutate (from (g g)) (to (c c)) (rate 0.0221172))
  (mutate (from (g g)) (to (g c)) (rate 0.315352))
  (mutate (from (g g)) (to (u c)) (rate 0.143198))
  (mutate (from (g g)) (to (a g)) (rate 0.364143))
  (mutate (from (g g)) (to (c g)) (rate 0.404881))
  (mutate (from (g g)) (to (u g)) (rate 0.21474))
  (mutate (from (g g)) (to (a u)) (rate 0.0294367))
  (mutate (from (g g)) (to (c u)) (rate 0.0639325))
  (mutate (from (g g)) (to (g u)) (rate 0.362801))
  (mutate (from (g g)) (to (u u)) (rate 0.118178))
  (mutate (from (u g)) (to (a a)) (rate 0.0177914))
  (mutate (from (u g)) (to (c a)) (rate 0.0373919))
  (mutate (from (u g)) (to (g a)) (rate 0.00580986))
  (mutate (from (u g)) (to (u a)) (rate 0.548891))
  (mutate (from (u g)) (to (a c)) (rate 0.00826519))
  (mutate (from (u g)) (to (c c)) (rate 0.00994823))
  (mutate (from (u g)) (to (g c)) (rate 0.0633766))
  (mutate (from (u g)) (to (u c)) (rate 0.0652568))
  (mutate (from (u g)) (to (a g)) (rate 0.057152))
  (mutate (from (u g)) (to (c g)) (rate 0.621343))
  (mutate (from (u g)) (to (g g)) (rate 0.0534378))
  (mutate (from (u g)) (to (a u)) (rate 0.0428718))
  (mutate (from (u g)) (to (c u)) (rate 0.0137622))
  (mutate (from (u g)) (to (g u)) (rate 0.040235))
  (mutate (from (u g)) (to (u u)) (rate 0.12103))
  (mutate (from (a u)) (to (a a)) (rate 0.0706289))
  (mutate (from (a u)) (to (c a)) (rate 0.00333792))
  (mutate (from (a u)) (to (g a)) (rate 0.00972485))
  (mutate (from (a u)) (to (u a)) (rate 0.227315))
  (mutate (from (a u)) (to (a c)) (rate 0.073575))
  (mutate (from (a u)) (to (c c)) (rate 0.00013534))
  (mutate (from (a u)) (to (g c)) (rate 0.466808))
  (mutate (from (a u)) (to (u c)) (rate 0.0110909))
  (mutate (from (a u)) (to (a g)) (rate 0.0398347))
  (mutate (from (a u)) (to (c g)) (rate 0.176274))
  (mutate (from (a u)) (to (g g)) (rate 0.00325686))
  (mutate (from (a u)) (to (u g)) (rate 0.019061))
  (mutate (from (a u)) (to (c u)) (rate 0.0267973))
  (mutate (from (a u)) (to (g u)) (rate 0.266126))
  (mutate (from (a u)) (to (u u)) (rate 0.0914102))
  (mutate (from (c u)) (to (a a)) (rate 0.124197))
  (mutate (from (c u)) (to (c a)) (rate 0.638811))
  (mutate (from (c u)) (to (g a)) (rate 0.0294746))
  (mutate (from (c u)) (to (u a)) (rate 0.0283935))
  (mutate (from (c u)) (to (a c)) (rate 0.0443892))
  (mutate (from (c u)) (to (c c)) (rate 0.883794))
  (mutate (from (c u)) (to (g c)) (rate 0.0650459))
  (mutate (from (c u)) (to (u c)) (rate 0.306403))
  (mutate (from (c u)) (to (a g)) (rate 0.0617594))
  (mutate (from (c u)) (to (c g)) (rate 0.508381))
  (mutate (from (c u)) (to (g g)) (rate 0.0903431))
  (mutate (from (c u)) (to (u g)) (rate 0.0781497))
  (mutate (from (c u)) (to (a u)) (rate 0.34226))
  (mutate (from (c u)) (to (g u)) (rate 0.415204))
  (mutate (from (c u)) (to (u u)) (rate 0.678589))
  (mutate (from (g u)) (to (a a)) (rate 0.0308204))
  (mutate (from (g u)) (to (c a)) (rate 0.0102598))
  (mutate (from (g u)) (to (g a)) (rate 0.092672))
  (mutate (from (g u)) (to (u a)) (rate 0.076055))
  (mutate (from (g u)) (to (a c)) (rate 0.0878171))
  (mutate (from (g u)) (to (c c)) (rate 0.00979718))
  (mutate (from (g u)) (to (g c)) (rate 0.831392))
  (mutate (from (g u)) (to (u c)) (rate 0.0132802))
  (mutate (from (g u)) (to (a g)) (rate 0.0196823))
  (mutate (from (g u)) (to (c g)) (rate 0.131798))
  (mutate (from (g u)) (to (g g)) (rate 0.111226))
  (mutate (from (g u)) (to (u g)) (rate 0.0495686))
  (mutate (from (g u)) (to (a u)) (rate 0.737425))
  (mutate (from (g u)) (to (c u)) (rate 0.0900796))
  (mutate (from (g u)) (to (u u)) (rate 0.107341))
  (mutate (from (u u)) (to (a a)) (rate 0.143335))
  (mutate (from (u u)) (to (c a)) (rate 0.0647381))
  (mutate (from (u u)) (to (g a)) (rate 0.0797961))
  (mutate (from (u u)) (to (u a)) (rate 0.661254))
  (mutate (from (u u)) (to (a c)) (rate 0.1423))
  (mutate (from (u u)) (to (c c)) (rate 0.0341837))
  (mutate (from (u u)) (to (g c)) (rate 0.0795004))
  (mutate (from (u u)) (to (u c)) (rate 0.476023))
  (mutate (from (u u)) (to (a g)) (rate 0.111179))
  (mutate (from (u u)) (to (c g)) (rate 0.11981))
  (mutate (from (u u)) (to (g g)) (rate 0.0877322))
  (mutate (from (u u)) (to (u g)) (rate 0.361059))
  (mutate (from (u u)) (to (a u)) (rate 0.613349))
  (mutate (from (u u)) (to (c u)) (rate 0.356496))
  (mutate (from (u u)) (to (g u)) (rate 0.259927))
 )  ;; end chain LNUC RNUC

 (chain
  (update-policy rev)
  (terminal (NUC))

  ;; initial probability distribution
  (initial (state (a)) (prob 0.316823))
  (initial (state (c)) (prob 0.191125))
  (initial (state (g)) (prob 0.231626))
  (initial (state (u)) (prob 0.260426))

  ;; mutation rates
  (mutate (from (a)) (to (c)) (rate 0.216179))
  (mutate (from (a)) (to (g)) (rate 0.323422))
  (mutate (from (a)) (to (u)) (rate 0.321388))
  (mutate (from (c)) (to (a)) (rate 0.358354))
  (mutate (from (c)) (to (g)) (rate 0.263416))
  (mutate (from (c)) (to (u)) (rate 0.728797))
  (mutate (from (g)) (to (a)) (rate 0.442384))
  (mutate (from (g)) (to (c)) (rate 0.217357))
  (mutate (from (g)) (to (u)) (rate 0.32297))
  (mutate (from (u)) (to (a)) (rate 0.390987))
  (mutate (from (u)) (to (c)) (rate 0.534862))
  (mutate (from (u)) (to (g)) (rate 0.287254))
 )  ;; end chain NUC

)  ;; end grammar pfold

;; Alphabet RNA
;;
(alphabet
 (name RNA)
 (token (a c g u))
 (complement (u g c a))
 (extend (to n) (from a) (from c) (from g) (from u))
 (extend (to x) (from a) (from c) (from g) (from u))
 (extend (to t) (from u))
 (extend (to r) (from a) (from g))
 (extend (to y) (from c) (from u))
 (extend (to m) (from a) (from c))
 (extend (to k) (from g) (from u))
 (extend (to s) (from c) (from g))
 (extend (to w) (from a) (from u))
 (extend (to h) (from a) (from c) (from u))
 (extend (to b) (from c) (from g) (from u))
 (extend (to v) (from a) (from c) (from g))
 (extend (to d) (from a) (from g) (from u))
 (wildcard *)
)  ;; end alphabet RNA