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;; phylocomposer example illustrating inference by dynamic programming
(token (A C G T))
(branch (name ROOT_BRANCH)
(sequence (A G G C C C A))
(transducer TKF91_ROOT)
(branch (transducer TKF91_BRANCH) (bit-profile (A G C ((C 1) (G 1)) A)))
(branch (transducer TKF91_BRANCH) (profile (((A .5)(C .5)) ((G .1)) C C A))))
(bit-value ((Qz A G) 1) ;; this label, Qz, isn't actually used anywhere; it's just assigned a value here to test the warning message
(beta 1)
(~beta 3))
(value ((Q A A) .75))
(value ((Q A C) .05))
(value ((Q A G) .15))
(value ((Q A T) .05))
(value ((Q C A) .05))
(value ((Q C C) .75))
(value ((Q C G) .05))
(value ((Q C T) .15))
(value ((Q G A) .15))
(value ((Q G C) .05))
(value ((Q G G) .75))
(value ((Q G T) .05))
(value ((Q T A) .05))
(value ((Q T C) .15))
(value ((Q T G) .05))
(value ((Q T T) .75))
(value ((pi A) .25))
(value ((pi C) .25))
(value ((pi G) .25))
(value ((pi T) .25))
(value ((del A) 1))
(value ((del C) 1))
(value ((del G) 1))
(value ((del T) 1))
(bit-value (alpha 1))
(bit-value (~alpha 1))
(bit-value (gamma 1))
(bit-value (~gamma 1))
(bit-value (kappa 1))
(bit-value (~kappa 1))
(transducer
(name TKF91_ROOT)
(state (name S) (type start))
(state (name E) (type end))
(state (name W) (type wait))
(state (name I) (type insert) (label pi))
(transition (from S) (to I) (label kappa))
(transition (from S) (to W) (label ~kappa))
(transition (from I) (to I) (label kappa))
(transition (from I) (to W) (label ~kappa))
(transition (from W) (to E)))
(transducer
(name TKF91_BRANCH)
(state (name S) (type start))
(state (name E) (type end))
(state (name W) (type wait))
(state (name M) (type match) (label Q))
(state (name D) (type delete) (label del))
(state (name I) (type insert) (label pi))
(transition (from S) (to I) (label beta))
(transition (from S) (to W) (label ~beta))
(transition (from W) (to M) (label alpha))
(transition (from W) (to D) (label ~alpha))
(transition (from W) (to E))
(transition (from M) (to I) (label beta))
(transition (from M) (to W) (label ~beta))
(transition (from D) (to I) (label gamma))
(transition (from D) (to W) (label ~gamma))
(transition (from I) (to I) (label beta))
(transition (from I) (to W) (label ~beta)))
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