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

[SETTINGS]
  [randomseed] 1568746 // seed for random generator so outputs can be checked

  /* 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 20]  // tree t1, model M0example1, root length 20
[PARTITIONS] pM0_2  [t2 M0example2 20]  // tree t2, model M0example2, root length 20
[PARTITIONS] pM0_3  [t3 M0example3 20]  // tree t3, model M0example3, root length 20
[PARTITIONS] pM0_4  [t4 M0example4 20]   // tree t4, model M0example4, root length 20

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

[EVOLVE] 
  pM0_1  5 out1  // 5 replicates generated from partition pM0_1 in file out1.fas etc
  pM0_2  5 out2  // 5 replicates generated from partition pM0_2 in file out2.fas etc
  pM0_3  5 out3  // 5 replicates generated from partition pM0_3 in file out3.fas etc
  pM0_4  5 out4  // 5 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

*/