/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  INDELible V1.03 control file - AMINOACID.txt                                   //
//                                                                                 //
//      An introduction to different amino-acid substitution models.               //
//                                                                                 //
/////////////////////////////////////////////////////////////////////////////////////

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

[TYPE] AMINOACID 1	//  amino-acid simulation using algorithm from method 1.

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

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

[MODEL]    JTTexample1
  [submodel]  JTT                     	//  JTT model defined using the code.

[MODEL]    JTTexample2
  [submodel]  1                       	//  JTT model defined using a number.

[MODEL]    WAGexample
  [submodel]  WAG                	//  WAG defined using the code

  /* Specifying stationary frequencies will force the +F version of a model */

[MODEL]    WAG_Fexample
  [submodel]  WAG                      // WAG+F
    [statefreq]                                         // list of 20 numbers 
      0.079066  0.055941  0.041977  0.053052  0.012937  // A R N D C  
      0.040767  0.071586  0.057337  0.022355  0.062157  // Q E G H I 
      0.099081  0.064600  0.022951  0.042302  0.044040  // L K M F P 
      0.061197  0.053287  0.012066  0.034155  0.069147  // S T W Y V

  /* User defined (reversible) amino-acid substitution model */

[MODEL]   USERexample                 // e.g. formatted like this
  [submodel]  userAAmodel.txt  	      // for the Dayhoff-dcmut model.

  /* 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] pJTT1  [t1 JTTexample1 160]  // tree t1, model JTTexample1, root length 160
[PARTITIONS] pJTT2  [t2 JTTexample2 500]  // tree t2, model JTTexample2, root length 500
[PARTITIONS] pWAG1  [t3 WAGexample 988]   // tree t3, model WAGexample, root length 988
[PARTITIONS] pWAG2  [t4 WAG_Fexample 75]  // tree t4, model WAG_Fexample, root length 75
[PARTITIONS] pUSER  [t3 USERexample 988]  // tree t3, model USERexample, root length 988

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

[EVOLVE] 
  pJTT1 5 J1out // 5 replicates generated from partition pJTT1 in file J1out.fas etc
  pJTT2 5 J2out // 5 replicates generated from partition pJTT2 in file J2out.fas etc
  pWAG1 5 Wout  // 5 replicates generated from partition pWAG1 in file Wout.fas etc
  pWAG2 5 WFout // 5 replicates generated from partition pWAG2 in file WFout.fas etc
  pUSER 5 Uout  // 5 replicates generated from partition pUSER in file Uout.fas etc

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

/*
     All amino-acid substitution models are specified as: [submodel] value
     where value is just an integer N or a code used to pick the amino-acid 
     substitution model as defined below (references given where appropriate):

    +-----+---------------+-------------------------------+
    |  N  | code          | Reference                     |
    +-----+---------------+-------------------------------+
    |  0  | Poisson       |  n/a                          |
    |  1  | JTT           |  Jones et al,. 1992           |
    |  2  | JTT-dcmut     |  Kosiol and Goldman, 2005     |
    |  3  | Dayhoff       |  Dayhoff et al., 1978         |
    |  4  | Dayhoff-dcmut |  Kosiol and Goldman, 2005     |
    |  5  | WAG           |  Whelan and Goldman, 2001     |
    |  6  | mtMAM         |  Yang et al., 1998            |
    |  7  | mtART         |  Abascal et al., 2007         |
    |  8  | mtREV         |  Adachi and Hasegawa, 1996    |
    |  9  | rtREV         |  Dimmic et al., 2002          |
    |  10 | cpREV         |  Adachi, 2000                 |
    |  11 | Vt            |  Muller and Vingron, 2000     |
    |  12 | Blosum        |  Henikoff and Henikoff, 1992  |
    |  13 | LG            |  Le and Gascuel, 2008         |
    |  14 | HIVb          |  Nickle et al., 2007          |
    |  15 | HIVw          |  Nickle et al., 2007          |
    |  16 | USER          |  n/a                          |
    +-----+---------------+-------------------------------+
   
    The only exception is the user-model where you simply specify the  
    name of the file that contains the state frequencies and the rate
    matrix Q. This file should be in the same folder as INDELible.

*/ 