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;; Grammar nullprot
;;
(grammar
(name nullprot)
(update-rates 1)
(update-rules 1)
;; Transformation rules for grammar symbols
;; State Start
;;
(transform (from (Start)) (to (S0)) (prob 0.5))
(transform (from (Start)) (to ()) (prob 0.5))
;; State S0
;;
(transform (from (S0)) (to (A0 S0*)) (gaps-ok)
(minlen 1))
(transform (from (S0*)) (to ()) (prob 0.5))
(transform (from (S0*)) (to (S0)) (prob 0.5))
;; Markov chain substitution models
(chain
(update-policy rev)
(terminal (A0))
;; initial probability distribution
(initial (state (a)) (prob 0.0962551))
(initial (state (r)) (prob 0.0373506))
(initial (state (n)) (prob 0.0422718))
(initial (state (d)) (prob 0.0405318))
(initial (state (c)) (prob 0.0266675))
(initial (state (q)) (prob 0.0336235))
(initial (state (e)) (prob 0.0466521))
(initial (state (g)) (prob 0.0716804))
(initial (state (h)) (prob 0.0308094))
(initial (state (i)) (prob 0.0301717))
(initial (state (l)) (prob 0.114685))
(initial (state (k)) (prob 0.0651995))
(initial (state (m)) (prob 0.0179707))
(initial (state (f)) (prob 0.0477261))
(initial (state (p)) (prob 0.0691653))
(initial (state (s)) (prob 0.0696891))
(initial (state (t)) (prob 0.0602472))
(initial (state (w)) (prob 0.00452625))
(initial (state (y)) (prob 0.0430247))
(initial (state (v)) (prob 0.0517526))
;; mutation rates
(mutate (from (a)) (to (r)) (rate 0.0137389))
(mutate (from (a)) (to (n)) (rate 0.032145))
(mutate (from (a)) (to (d)) (rate 0.0290394))
(mutate (from (a)) (to (c)) (rate 0.0120395))
(mutate (from (a)) (to (q)) (rate 0.0173705))
(mutate (from (a)) (to (e)) (rate 0.11368))
(mutate (from (a)) (to (g)) (rate 0.233484))
(mutate (from (a)) (to (h)) (rate 0.00819576))
(mutate (from (a)) (to (i)) (rate 0.0104437))
(mutate (from (a)) (to (l)) (rate 0.0382806))
(mutate (from (a)) (to (k)) (rate 0.013646))
(mutate (from (a)) (to (m)) (rate 0.010476))
(mutate (from (a)) (to (f)) (rate 0.00579197))
(mutate (from (a)) (to (p)) (rate 0.156722))
(mutate (from (a)) (to (s)) (rate 0.230172))
(mutate (from (a)) (to (t)) (rate 0.182034))
(mutate (from (a)) (to (w)) (rate 0.000225972))
(mutate (from (a)) (to (y)) (rate 0.0109928))
(mutate (from (a)) (to (v)) (rate 0.130478))
(mutate (from (r)) (to (a)) (rate 0.0354062))
(mutate (from (r)) (to (d)) (rate 0.00293112))
(mutate (from (r)) (to (c)) (rate 0.00566818))
(mutate (from (r)) (to (q)) (rate 0.108957))
(mutate (from (r)) (to (e)) (rate 0.00321786))
(mutate (from (r)) (to (g)) (rate 0.00236413))
(mutate (from (r)) (to (h)) (rate 0.0941947))
(mutate (from (r)) (to (i)) (rate 0.0209864))
(mutate (from (r)) (to (l)) (rate 0.00611536))
(mutate (from (r)) (to (k)) (rate 0.320363))
(mutate (from (r)) (to (m)) (rate 0.019884))
(mutate (from (r)) (to (f)) (rate 0.00410899))
(mutate (from (r)) (to (p)) (rate 0.0639268))
(mutate (from (r)) (to (s)) (rate 0.104307))
(mutate (from (r)) (to (t)) (rate 0.00539579))
(mutate (from (r)) (to (w)) (rate 0.0179838))
(mutate (from (r)) (to (y)) (rate 0.0025521))
(mutate (from (r)) (to (v)) (rate 0.0135736))
(mutate (from (n)) (to (a)) (rate 0.0731959))
(mutate (from (n)) (to (d)) (rate 0.545267))
(mutate (from (n)) (to (c)) (rate 0.0016541))
(mutate (from (n)) (to (q)) (rate 0.00610871))
(mutate (from (n)) (to (e)) (rate 0.0133541))
(mutate (from (n)) (to (g)) (rate 0.0849646))
(mutate (from (n)) (to (h)) (rate 0.208984))
(mutate (from (n)) (to (i)) (rate 0.0169964))
(mutate (from (n)) (to (l)) (rate 0.0287232))
(mutate (from (n)) (to (k)) (rate 0.273209))
(mutate (from (n)) (to (f)) (rate 0.00411821))
(mutate (from (n)) (to (p)) (rate 0.0271662))
(mutate (from (n)) (to (s)) (rate 0.314662))
(mutate (from (n)) (to (t)) (rate 0.115505))
(mutate (from (n)) (to (w)) (rate 0.00161367))
(mutate (from (n)) (to (y)) (rate 0.0343259))
(mutate (from (n)) (to (v)) (rate 0.0212746))
(mutate (from (d)) (to (a)) (rate 0.068963))
(mutate (from (d)) (to (r)) (rate 0.00270107))
(mutate (from (d)) (to (n)) (rate 0.568675))
(mutate (from (d)) (to (c)) (rate 0.00217445))
(mutate (from (d)) (to (q)) (rate 0.0192285))
(mutate (from (d)) (to (e)) (rate 0.953904))
(mutate (from (d)) (to (g)) (rate 0.0934063))
(mutate (from (d)) (to (h)) (rate 0.00694097))
(mutate (from (d)) (to (i)) (rate 0.00592246))
(mutate (from (d)) (to (l)) (rate 0.00284149))
(mutate (from (d)) (to (k)) (rate 0.0497658))
(mutate (from (d)) (to (m)) (rate 0.00166883))
(mutate (from (d)) (to (f)) (rate 0.00124454))
(mutate (from (d)) (to (p)) (rate 0.0124936))
(mutate (from (d)) (to (s)) (rate 0.0373232))
(mutate (from (d)) (to (t)) (rate 0.0253135))
(mutate (from (d)) (to (v)) (rate 0.00819178))
(mutate (from (c)) (to (a)) (rate 0.043456))
(mutate (from (c)) (to (r)) (rate 0.00793886))
(mutate (from (c)) (to (n)) (rate 0.00262197))
(mutate (from (c)) (to (d)) (rate 0.00330493))
(mutate (from (c)) (to (g)) (rate 0.0110151))
(mutate (from (c)) (to (h)) (rate 0.0125032))
(mutate (from (c)) (to (i)) (rate 0.0200569))
(mutate (from (c)) (to (l)) (rate 1.50702e-05))
(mutate (from (c)) (to (m)) (rate 0.000353939))
(mutate (from (c)) (to (p)) (rate 0.0147209))
(mutate (from (c)) (to (s)) (rate 0.107316))
(mutate (from (c)) (to (t)) (rate 0.00611114))
(mutate (from (c)) (to (w)) (rate 6.57388e-05))
(mutate (from (c)) (to (y)) (rate 0.038097))
(mutate (from (c)) (to (v)) (rate 0.0314731))
(mutate (from (q)) (to (a)) (rate 0.0497271))
(mutate (from (q)) (to (r)) (rate 0.121035))
(mutate (from (q)) (to (n)) (rate 0.00767994))
(mutate (from (q)) (to (d)) (rate 0.0231792))
(mutate (from (q)) (to (e)) (rate 0.348695))
(mutate (from (q)) (to (g)) (rate 0.0319475))
(mutate (from (q)) (to (h)) (rate 0.278544))
(mutate (from (q)) (to (i)) (rate 0.00137544))
(mutate (from (q)) (to (l)) (rate 0.0899005))
(mutate (from (q)) (to (k)) (rate 0.154502))
(mutate (from (q)) (to (m)) (rate 0.0122557))
(mutate (from (q)) (to (p)) (rate 0.0705534))
(mutate (from (q)) (to (s)) (rate 0.0427736))
(mutate (from (q)) (to (t)) (rate 0.0516448))
(mutate (from (q)) (to (v)) (rate 0.031027))
(mutate (from (e)) (to (a)) (rate 0.23455))
(mutate (from (e)) (to (r)) (rate 0.00257628))
(mutate (from (e)) (to (n)) (rate 0.0121002))
(mutate (from (e)) (to (d)) (rate 0.82876))
(mutate (from (e)) (to (q)) (rate 0.251314))
(mutate (from (e)) (to (g)) (rate 0.0786291))
(mutate (from (e)) (to (h)) (rate 0.0180443))
(mutate (from (e)) (to (i)) (rate 0.0249968))
(mutate (from (e)) (to (l)) (rate 0.0079022))
(mutate (from (e)) (to (k)) (rate 0.0855621))
(mutate (from (e)) (to (m)) (rate 0.00238415))
(mutate (from (e)) (to (p)) (rate 0.0303577))
(mutate (from (e)) (to (s)) (rate 0.0849887))
(mutate (from (e)) (to (t)) (rate 0.0179829))
(mutate (from (e)) (to (w)) (rate 5.20212e-05))
(mutate (from (e)) (to (y)) (rate 0.00978899))
(mutate (from (e)) (to (v)) (rate 0.023213))
(mutate (from (g)) (to (a)) (rate 0.313531))
(mutate (from (g)) (to (r)) (rate 0.00123188))
(mutate (from (g)) (to (n)) (rate 0.0501058))
(mutate (from (g)) (to (d)) (rate 0.0528166))
(mutate (from (g)) (to (c)) (rate 0.00409798))
(mutate (from (g)) (to (q)) (rate 0.0149857))
(mutate (from (g)) (to (e)) (rate 0.0511745))
(mutate (from (g)) (to (h)) (rate 0.00540573))
(mutate (from (g)) (to (i)) (rate 0.00245469))
(mutate (from (g)) (to (l)) (rate 0.00559022))
(mutate (from (g)) (to (k)) (rate 0.0330404))
(mutate (from (g)) (to (m)) (rate 0.00495194))
(mutate (from (g)) (to (f)) (rate 0.00635179))
(mutate (from (g)) (to (p)) (rate 0.0261705))
(mutate (from (g)) (to (s)) (rate 0.151741))
(mutate (from (g)) (to (t)) (rate 0.0131432))
(mutate (from (g)) (to (y)) (rate 0.000525532))
(mutate (from (g)) (to (v)) (rate 0.0226539))
(mutate (from (h)) (to (a)) (rate 0.0256053))
(mutate (from (h)) (to (r)) (rate 0.114193))
(mutate (from (h)) (to (n)) (rate 0.286734))
(mutate (from (h)) (to (d)) (rate 0.00913131))
(mutate (from (h)) (to (c)) (rate 0.0108223))
(mutate (from (h)) (to (q)) (rate 0.303986))
(mutate (from (h)) (to (e)) (rate 0.0273231))
(mutate (from (h)) (to (g)) (rate 0.0125768))
(mutate (from (h)) (to (i)) (rate 0.00618497))
(mutate (from (h)) (to (l)) (rate 0.0428964))
(mutate (from (h)) (to (k)) (rate 0.00617126))
(mutate (from (h)) (to (m)) (rate 0.00157941))
(mutate (from (h)) (to (f)) (rate 0.0222249))
(mutate (from (h)) (to (p)) (rate 0.0660071))
(mutate (from (h)) (to (s)) (rate 0.0300311))
(mutate (from (h)) (to (t)) (rate 0.0107019))
(mutate (from (h)) (to (w)) (rate 0.00187191))
(mutate (from (h)) (to (y)) (rate 0.0436021))
(mutate (from (h)) (to (v)) (rate 0.0336793))
(mutate (from (i)) (to (a)) (rate 0.033318))
(mutate (from (i)) (to (r)) (rate 0.0259798))
(mutate (from (i)) (to (n)) (rate 0.0238126))
(mutate (from (i)) (to (d)) (rate 0.00795606))
(mutate (from (i)) (to (c)) (rate 0.0177275))
(mutate (from (i)) (to (q)) (rate 0.0015328))
(mutate (from (i)) (to (e)) (rate 0.0386506))
(mutate (from (i)) (to (g)) (rate 0.00583173))
(mutate (from (i)) (to (h)) (rate 0.0063157))
(mutate (from (i)) (to (l)) (rate 0.276859))
(mutate (from (i)) (to (k)) (rate 0.0419729))
(mutate (from (i)) (to (m)) (rate 0.0460178))
(mutate (from (i)) (to (f)) (rate 0.0941424))
(mutate (from (i)) (to (p)) (rate 0.0132364))
(mutate (from (i)) (to (s)) (rate 0.00744573))
(mutate (from (i)) (to (t)) (rate 0.154455))
(mutate (from (i)) (to (w)) (rate 0.000143525))
(mutate (from (i)) (to (y)) (rate 0.0118211))
(mutate (from (i)) (to (v)) (rate 0.555768))
(mutate (from (l)) (to (a)) (rate 0.0321288))
(mutate (from (l)) (to (r)) (rate 0.00199165))
(mutate (from (l)) (to (n)) (rate 0.0105871))
(mutate (from (l)) (to (d)) (rate 0.00100423))
(mutate (from (l)) (to (c)) (rate 3.50424e-06))
(mutate (from (l)) (to (q)) (rate 0.0263571))
(mutate (from (l)) (to (e)) (rate 0.00321449))
(mutate (from (l)) (to (g)) (rate 0.00349399))
(mutate (from (l)) (to (h)) (rate 0.0115238))
(mutate (from (l)) (to (i)) (rate 0.0728367))
(mutate (from (l)) (to (k)) (rate 0.0135149))
(mutate (from (l)) (to (m)) (rate 0.0777009))
(mutate (from (l)) (to (f)) (rate 0.0509868))
(mutate (from (l)) (to (p)) (rate 0.0120491))
(mutate (from (l)) (to (s)) (rate 0.0144089))
(mutate (from (l)) (to (t)) (rate 0.0145428))
(mutate (from (l)) (to (w)) (rate 0.00278835))
(mutate (from (l)) (to (y)) (rate 0.00886752))
(mutate (from (l)) (to (v)) (rate 0.0726127))
(mutate (from (k)) (to (a)) (rate 0.0201458))
(mutate (from (k)) (to (r)) (rate 0.183525))
(mutate (from (k)) (to (n)) (rate 0.177134))
(mutate (from (k)) (to (d)) (rate 0.0309373))
(mutate (from (k)) (to (q)) (rate 0.0796767))
(mutate (from (k)) (to (e)) (rate 0.0612221))
(mutate (from (k)) (to (g)) (rate 0.0363247))
(mutate (from (k)) (to (h)) (rate 0.00291616))
(mutate (from (k)) (to (i)) (rate 0.0194233))
(mutate (from (k)) (to (l)) (rate 0.0237726))
(mutate (from (k)) (to (m)) (rate 0.0399115))
(mutate (from (k)) (to (f)) (rate 0.00150391))
(mutate (from (k)) (to (p)) (rate 0.0198995))
(mutate (from (k)) (to (s)) (rate 0.0851466))
(mutate (from (k)) (to (t)) (rate 0.0804877))
(mutate (from (k)) (to (y)) (rate 0.00314481))
(mutate (from (k)) (to (v)) (rate 0.0105565))
(mutate (from (m)) (to (a)) (rate 0.0561118))
(mutate (from (m)) (to (r)) (rate 0.0413271))
(mutate (from (m)) (to (d)) (rate 0.00376392))
(mutate (from (m)) (to (c)) (rate 0.000525225))
(mutate (from (m)) (to (q)) (rate 0.0229306))
(mutate (from (m)) (to (e)) (rate 0.00618926))
(mutate (from (m)) (to (g)) (rate 0.019752))
(mutate (from (m)) (to (h)) (rate 0.00270776))
(mutate (from (m)) (to (i)) (rate 0.0772608))
(mutate (from (m)) (to (l)) (rate 0.495869))
(mutate (from (m)) (to (k)) (rate 0.144803))
(mutate (from (m)) (to (f)) (rate 0.0378644))
(mutate (from (m)) (to (p)) (rate 0.00768306))
(mutate (from (m)) (to (s)) (rate 0.0147427))
(mutate (from (m)) (to (t)) (rate 0.0674563))
(mutate (from (m)) (to (w)) (rate 4.36172e-05))
(mutate (from (m)) (to (y)) (rate 7.25993e-05))
(mutate (from (m)) (to (v)) (rate 0.156444))
(mutate (from (f)) (to (a)) (rate 0.0116814))
(mutate (from (f)) (to (r)) (rate 0.00321571))
(mutate (from (f)) (to (n)) (rate 0.00364757))
(mutate (from (f)) (to (d)) (rate 0.00105694))
(mutate (from (f)) (to (g)) (rate 0.00953984))
(mutate (from (f)) (to (h)) (rate 0.0143472))
(mutate (from (f)) (to (i)) (rate 0.0595153))
(mutate (from (f)) (to (l)) (rate 0.122521))
(mutate (from (f)) (to (k)) (rate 0.00205452))
(mutate (from (f)) (to (m)) (rate 0.0142574))
(mutate (from (f)) (to (p)) (rate 0.00519238))
(mutate (from (f)) (to (s)) (rate 0.0256277))
(mutate (from (f)) (to (t)) (rate 0.00336955))
(mutate (from (f)) (to (w)) (rate 0.00615415))
(mutate (from (f)) (to (y)) (rate 0.20086))
(mutate (from (f)) (to (v)) (rate 0.0129986))
(mutate (from (p)) (to (a)) (rate 0.218105))
(mutate (from (p)) (to (r)) (rate 0.0345217))
(mutate (from (p)) (to (n)) (rate 0.0166032))
(mutate (from (p)) (to (d)) (rate 0.00732138))
(mutate (from (p)) (to (c)) (rate 0.00567581))
(mutate (from (p)) (to (q)) (rate 0.0342983))
(mutate (from (p)) (to (e)) (rate 0.0204763))
(mutate (from (p)) (to (g)) (rate 0.0271222))
(mutate (from (p)) (to (h)) (rate 0.0294026))
(mutate (from (p)) (to (i)) (rate 0.00577406))
(mutate (from (p)) (to (l)) (rate 0.019979))
(mutate (from (p)) (to (k)) (rate 0.0187585))
(mutate (from (p)) (to (m)) (rate 0.00199624))
(mutate (from (p)) (to (f)) (rate 0.00358289))
(mutate (from (p)) (to (s)) (rate 0.102331))
(mutate (from (p)) (to (t)) (rate 0.0371096))
(mutate (from (p)) (to (w)) (rate 0.000122152))
(mutate (from (p)) (to (v)) (rate 0.012666))
(mutate (from (s)) (to (a)) (rate 0.317915))
(mutate (from (s)) (to (r)) (rate 0.0559046))
(mutate (from (s)) (to (n)) (rate 0.190866))
(mutate (from (s)) (to (d)) (rate 0.0217075))
(mutate (from (s)) (to (c)) (rate 0.0410662))
(mutate (from (s)) (to (q)) (rate 0.0206373))
(mutate (from (s)) (to (e)) (rate 0.0568941))
(mutate (from (s)) (to (g)) (rate 0.156077))
(mutate (from (s)) (to (h)) (rate 0.0132767))
(mutate (from (s)) (to (i)) (rate 0.00322361))
(mutate (from (s)) (to (l)) (rate 0.0237123))
(mutate (from (s)) (to (k)) (rate 0.0796612))
(mutate (from (s)) (to (m)) (rate 0.0038017))
(mutate (from (s)) (to (f)) (rate 0.0175509))
(mutate (from (s)) (to (p)) (rate 0.101561))
(mutate (from (s)) (to (t)) (rate 0.364279))
(mutate (from (s)) (to (w)) (rate 0.00466144))
(mutate (from (s)) (to (y)) (rate 0.00835936))
(mutate (from (s)) (to (v)) (rate 0.0286679))
(mutate (from (t)) (to (a)) (rate 0.290831))
(mutate (from (t)) (to (r)) (rate 0.00334515))
(mutate (from (t)) (to (n)) (rate 0.0810426))
(mutate (from (t)) (to (d)) (rate 0.0170299))
(mutate (from (t)) (to (c)) (rate 0.00270501))
(mutate (from (t)) (to (q)) (rate 0.0288226))
(mutate (from (t)) (to (e)) (rate 0.0139249))
(mutate (from (t)) (to (g)) (rate 0.0156375))
(mutate (from (t)) (to (h)) (rate 0.00547277))
(mutate (from (t)) (to (i)) (rate 0.0773507))
(mutate (from (t)) (to (l)) (rate 0.0276833))
(mutate (from (t)) (to (k)) (rate 0.0871038))
(mutate (from (t)) (to (m)) (rate 0.0201211))
(mutate (from (t)) (to (f)) (rate 0.00266926))
(mutate (from (t)) (to (p)) (rate 0.0426028))
(mutate (from (t)) (to (s)) (rate 0.421369))
(mutate (from (t)) (to (y)) (rate 0.0100259))
(mutate (from (t)) (to (v)) (rate 0.112892))
(mutate (from (w)) (to (a)) (rate 0.00480552))
(mutate (from (w)) (to (r)) (rate 0.148402))
(mutate (from (w)) (to (n)) (rate 0.0150705))
(mutate (from (w)) (to (c)) (rate 0.000387317))
(mutate (from (w)) (to (e)) (rate 0.000536183))
(mutate (from (w)) (to (h)) (rate 0.0127417))
(mutate (from (w)) (to (i)) (rate 0.00095673))
(mutate (from (w)) (to (l)) (rate 0.0706506))
(mutate (from (w)) (to (m)) (rate 0.000173175))
(mutate (from (w)) (to (f)) (rate 0.0648911))
(mutate (from (w)) (to (p)) (rate 0.0018666))
(mutate (from (w)) (to (s)) (rate 0.0717707))
(mutate (from (w)) (to (y)) (rate 0.0322862))
(mutate (from (y)) (to (a)) (rate 0.0245932))
(mutate (from (y)) (to (r)) (rate 0.00221553))
(mutate (from (y)) (to (n)) (rate 0.0337252))
(mutate (from (y)) (to (c)) (rate 0.0236133))
(mutate (from (y)) (to (e)) (rate 0.0106143))
(mutate (from (y)) (to (g)) (rate 0.000875552))
(mutate (from (y)) (to (h)) (rate 0.0312228))
(mutate (from (y)) (to (i)) (rate 0.00828968))
(mutate (from (y)) (to (l)) (rate 0.023637))
(mutate (from (y)) (to (k)) (rate 0.00476564))
(mutate (from (y)) (to (m)) (rate 3.03236e-05))
(mutate (from (y)) (to (f)) (rate 0.222809))
(mutate (from (y)) (to (s)) (rate 0.01354))
(mutate (from (y)) (to (t)) (rate 0.0140393))
(mutate (from (y)) (to (w)) (rate 0.00339655))
(mutate (from (y)) (to (v)) (rate 0.0126108))
(mutate (from (v)) (to (a)) (rate 0.242676))
(mutate (from (v)) (to (r)) (rate 0.00979627))
(mutate (from (v)) (to (n)) (rate 0.0173772))
(mutate (from (v)) (to (d)) (rate 0.00641566))
(mutate (from (v)) (to (c)) (rate 0.0162178))
(mutate (from (v)) (to (q)) (rate 0.0201581))
(mutate (from (v)) (to (e)) (rate 0.0209253))
(mutate (from (v)) (to (g)) (rate 0.031377))
(mutate (from (v)) (to (h)) (rate 0.02005))
(mutate (from (v)) (to (i)) (rate 0.324012))
(mutate (from (v)) (to (l)) (rate 0.160912))
(mutate (from (v)) (to (k)) (rate 0.0132994))
(mutate (from (v)) (to (m)) (rate 0.0543241))
(mutate (from (v)) (to (f)) (rate 0.0119872))
(mutate (from (v)) (to (p)) (rate 0.0169276))
(mutate (from (v)) (to (s)) (rate 0.0386037))
(mutate (from (v)) (to (t)) (rate 0.131422))
(mutate (from (v)) (to (y)) (rate 0.010484))
) ;; end chain A0
) ;; end grammar nullprot
;; Alphabet Protein
;;
(alphabet
(name Protein)
(token (a r n d c q e g h i l k m f p s t w y v))
(extend (to x) (from a) (from r) (from n) (from d) (from c) (from q) (from e) (from g) (from h) (from i) (from l) (from k) (from m) (from f) (from p) (from s) (from t) (from w) (from y) (from v))
(extend (to b) (from n) (from d))
(extend (to z) (from q) (from e))
(wildcard *)
) ;; end alphabet Protein