    /////////////////////////////////////////////////////////////////////////////////////
    //                                                                                 //
    //  INDELible V1.03 control file - CODON.txt                                       //
    //                                                                                 //
    //      An introduction to codon substitution models.                              //
    //                                                                                 //
    /////////////////////////////////////////////////////////////////////////////////////

      /* Again - the control file must begin with the [TYPE] statement */

    [TYPE] CODON 2	//  codon simulation using algorithm from method 2

      /* Many different models can be defined in a single control file */

    [MODEL] M0example1
        [submodel]  2.5  0.5                     //  kappa=2.5, w=0.5

    [MODEL] M0example2
        [submodel]  5.0  1.0                     //  kappa=5.0, w=1.0

      /* The genetic code is the standard code by default but can be changed, e.g. */

    [MODEL] M0example3
        [submodel]     2.5  0.5                  //  kappa=2.5, w=0.5
        [geneticcode]  3                         //  The Yeast Mitochondrial Code
                                                 //  (see end of file for more)

      /* The stationary frequencies are set equal by default but can be changed, e.g. */
      /* (Notice how the stop codons for this genetic code have a value of zero). */

    [MODEL] M0example4
        [submodel]     2.5  0.5                  //  kappa=2.5, w=0.5
        [statefreq]
          0.016133 0.014626 0.012261 0.019123    //  TTT  TTC  TTA  TTG
          0.008365 0.007583 0.006357 0.009915    //  TCT  TCC  TCA  TCG
          0.013290 0.012048 0        0           //  TAT  TAC  TAA  TAG
          0.009947 0.009018 0        0.011790    //  TGT  TGC  TGA  TGG

          0.019297 0.017494 0.014665 0.022873    //  CTT  CTC  CTA  CTG
          0.010005 0.009070 0.007604 0.011859    //  CCT  CCC  CCA  CCG
          0.015896 0.014410 0.012080 0.018841    //  CAT  CAC  CAA  CAG
          0.011898 0.010786 0.009042 0.014102    //  CGT  CGC  CGA  CGG

          0.030728 0.027857 0.023353 0.036422    //  ATT  ATC  ATA  ATG
          0.015932 0.014443 0.012108 0.018884    //  ACT  ACC  ACA  ACG
          0.025312 0.022947 0.019236 0.030002    //  AAT  AAC  AAA  AAG
          0.018945 0.017175 0.014398 0.022456    //  AGT  AGC  AGA  AGG

          0.024518 0.022227 0.018633 0.029061    //  GTT  GTC  GTA  GTG
          0.012712 0.011524 0.009661 0.015068    //  GCT  GCC  GCA  GCG
          0.020196 0.018309 0.015349 0.023938    //  GAT  GAC  GAA  GAG
          0.015117 0.013704 0.011488 0.017919    //  GGT  GGC  GGA  GGG

      /* Many different trees can be defined in a single control file */

    [TREE] t1  (A:0.1,B:0.1);
    [TREE] t2  ( (A:0.1, B:0.1):0.1, (C:0.3, D:0.3):0.5 );
    [TREE] t3  ( species1:0.1, species2:0.1, (species3:0.2, species4:0.2):0.01 );
    [TREE] t4
     (((1:0.1,2:0.1):0.1,(3:0.1,4:0.1):0.1):0.1,((5:0.1,6:0.1):0.1,(7:0.1,8:0.1):0.1):0.1);

      /* Many different partition groupings can be defined in a single control file */

    [PARTITIONS] pM0_1  [t1 M0example1 160]  // tree t1, model M0example1, root length 160
    [PARTITIONS] pM0_2  [t2 M0example2 500]  // tree t2, model M0example2, root length 500
    [PARTITIONS] pM0_3  [t3 M0example3 988]  // tree t3, model M0example3, root length 988
    [PARTITIONS] pM0_4  [t4 M0example4 75]   // tree t4, model M0example4, root length 75

      /* The [EVOLVE] statement is then used to list all the simulations you want to do */

    [EVOLVE]
      pM0_1  40 out1  // 40 replicates generated from partition pM0_1 in file out1.fas etc
      pM0_2  50 out2  // 50 replicates generated from partition pM0_2 in file out2.fas etc
      pM0_3  25 out3  // 25 replicates generated from partition pM0_3 in file out3.fas etc
      pM0_4  10 out4  // 10 replicates generated from partition pM0_4 in file out4.fas etc

    /////////////////////////////////////////////////////////////////////////////////////

    /*
        Codon frequencies are changed from being equal by listing 64 numbers (separated
        by white space) after the command [statefreq].

        The genetic code is changed using the command [geneticcode].

        e.g. [geneticcode] 3

        The value should be an integer 1 to 6, 9 to 16, or 21 to 24, corresponding to the
        genetic codes listed on Genbank. The value 1 (corresponding to the universal genetic
        code) is the default setting if the command is not specified.

        These genetic codes determine which codons are stop codons and therefore not
        included in the simulation. They are also used to translate codons to amino-acids
        for output if that option is chosen.  The codes listed at Genbank (in Oct. 2008)
        are given below (* represents a stop codon). Please note that some codes listed
        are identical and only differ in terms of Starts. For more info. visit Genbank.

           1  - The Standard Code
           FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           2  - The Vertebrate Mitochondrial Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
           3  - The Yeast Mitochondrial Code
           FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           4  - The Mold, Protozoan, and Coelenterate Mitochondrial
                Code and the Mycoplasma/Spiroplasma Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           5  - The Invertebrate Mitochondrial Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
           6  - The Ciliate, Dasycladacean and Hexamita Nuclear Code
           FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           9  - The Echinoderm and Flatworm Mitochondrial Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
           10 - The Euplotid Nuclear Code
           FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           11 - The Bacterial and Plant Plastid Code
           FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           12 - The Alternative Yeast Nuclear Code
           FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           13 - The Ascidian Mitochondrial Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
           14 - The Alternative Flatworm Mitochondrial Code
           FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
           15 - The Blepharisma Nuclear Code
           FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           16 - The Chlorophycean Mitochondrial Code
           FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           21 - The Trematode Mitochondrial Code
           FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
           22 - The Scenedesmus obliquus mitochondrial Code
           FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
           23 - The Thraustochytrium Mitochondrial Code
           FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG

    Base1: TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
    Base2: TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
    Base3: TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

    */