[TYPE] NUCLEOTIDE 2	//  nucleotide simulation using algorithm from method 2.
[MODEL]    HKY2
  [submodel]  HKY 2                	//  HKY with a=f=kappa=2.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY2.5
  [submodel]  HKY 2.5                	//  HKY with a=f=kappa=1.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY3
  [submodel]  HKY 3                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY3.5
  [submodel]  HKY 3.5                	//  HKY with a=f=kappa=2.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY4
  [submodel]  HKY 4                	//  HKY with a=f=kappa=1.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY4.5
  [submodel]  HKY 4.5                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY5
  [submodel]  HKY 5                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY5.5
  [submodel]  HKY 5.5                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY6
  [submodel]  HKY 6                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
[MODEL]    HKY6.5
  [submodel]  HKY 6.5                	//  HKY with a=f=kappa=3.5, b=c=d=e=1
  [statefreq] 0.3 0.2 0.3 0.2    // T,C,A,G
  [indelmodel]  POW  2 100 //  Power law insertion/deletion length distribution (a=2)
  [indelrate]   0.005          //  insertion rate = deletion rate = 0.05
                             //  relative to average substitution rate of 1.   
// Symmetric tree
[TREE] tree24Sym
((((H1:0.15,G1:0.15):0.15,(F1:0.15,E1:0.15):0.15:0.15):0.15,((D1:0.15,C1:0.15):0.15,(B1:0.15,A1:0.15):0.15:0.15):0.15:0.15):0.15,(((H2:0.15,G2:0.15):0.15,(F2:0.15,E2:0.15):0.15:0.15):0.15,((D2:0.15,C2:0.15):0.15,(B2:0.15,A2:0.15):0.15:0.15):0.15:0.15):0.15,(((H3:0.15,G3:0.15):0.15,(F3:0.15,E3:0.15):0.15:0.15):0.15,((D3:0.15,C3:0.15):0.15,(B3:0.15,A3:0.15):0.15:0.15):0.15:0.15):0.15:0.15);

[PARTITIONS] pHKY85Sym2.5  [tree24Sym HKY2.5 500] 
[PARTITIONS] pHKY85Sym3  [tree24Sym HKY3 500] 
[PARTITIONS] pHKY85Sym3.5  [tree24Sym HKY3.5 500] 
[PARTITIONS] pHKY85Sym4  [tree24Sym HKY4 500] 
[PARTITIONS] pHKY85Sym4.5  [tree24Sym HKY4.5 500] 
[PARTITIONS] pHKY85Sym5  [tree24Sym HKY5 500] 
[PARTITIONS] pHKY85Sym5.5  [tree24Sym HKY5.5 500] 
[PARTITIONS] pHKY85Sym6  [tree24Sym HKY6 500] 
[PARTITIONS] pHKY85Sym6.5  [tree24Sym HKY6.5 500] 

[EVOLVE] 
  pHKY85Sym2 100 HKYSym2
  pHKY85Sym2.5 100 HKYSym2.5
  pHKY85Sym3 100 HKYSym3
  pHKY85Sym3.5 100 HKYSym3.5
  pHKY85Sym4 100 HKYSym4
  pHKY85Sym4.5 100 HKYSym4.5
  pHKY85Sym5 100 HKYSym5
  pHKY85Sym5.5 100 HKYSym5.5
  pHKY85Sym6 100 HKYSym6
  pHKY85Sym6.5 100 HKYSym6.5