model {
    for(k in 1:K){
      beta[k] <- alpha[2,k]/sum(alpha[2,1:K]) - alpha[1,k]/sum(alpha[1,1:K])
    }

    for(i in 1:I1){
      ## reference group
      for(n in 1:N1[i]){
        xG1[n,1,i] ~ dcat(pStates1[1, 1:numStates, sCat1[i,n]])
        for(h in 1:numFlank){
          xG1[n,h+1,i] ~ dcat(pStates2[h, 1:numFlank, sCat1[i,n]])
        }
        xG1[n,numFlank+2,i] ~ dcat(pStates3[1, 1:2, sCat1[i,n]])

        sCat1[i,n] ~ dcat(p1[i,1:K])
      }

      p1[i,1:K] ~ ddirch(alpha[1,1:K])

    }

    for(i in 1:I2){
      ## the other group
      for(n in 1:N2[i]){
        xG2[n,1,i] ~ dcat(pStates1[1, 1:numStates, sCat2[i,n]])
        for(h in 1:numFlank){
          xG2[n,h+1,i] ~ dcat(pStates2[h, 1:numFlank, sCat2[i,n]])
        }
        xG2[n,numFlank+2,i] ~ dcat(pStates3[1, 1:2, sCat2[i,n]])

        sCat2[i,n] ~ dcat(p2[i,1:K])
      }

      p2[i,1:K] ~ ddirch(alpha[2,1:K])
    }

    ## priors
    alpha[1,1:K] <- gamma[1]*mu[1,1:K]
    alpha[2,1:K] <- gamma[2]*mu[M,1:K]

    mu[1,1:K] ~ ddirch(a[1:K])
    mu[2,1:K] ~ ddirch(a[1:K])

    for(k in 1:K) {
      a[k] <- 1
    }

    gamma[1] ~ dgamma(0.001,0.001)
    gamma[2] ~ dgamma(0.001,0.001)


    ## signatures
    for(k in 1:K) {
      ## substituion type
      pStates1[1,1:numStates,k] ~ ddirch(gammas1[1:numStates])

      ## flanking bases
      for(w in 1:numFlank){
        pStates2[w,1:numFlank,k] ~ ddirch(gammas2[1:numFlank])
      }

      pStates3[1,1:2,k] ~ ddirch(gammas3[1:2])
    }

    ## priors
    for(q in 1:numStates){
        gammas1[q] <- 1
    }

    for(h in 1:numFlank){
        gammas2[h] <- 1
    }

    gammas3[1:2] <- c(1,1)

    ## model indicator
    M ~ dcat(prob[])
    prob[1] <- prob1
    prob[2] <- 1-prob[1]
    pM2 <- step(M - 1.5)
}
