/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  INDELible V1.03 control file - basic.txt                                       //
//                                                                                 //
//      A basic introduction to the structure of the INDELible control file.       //
//                                                                                 //
//      There are other examples in the file examples.html in the help folder      //
//      Any one of those examples will work if cut and paste into a control file.  //
//                                                                                 //
/////////////////////////////////////////////////////////////////////////////////////

// It is useful to know that anything on a line after two forward slashes is ignored.

/*
   Another useful thing to know is that anything after a forward slash and star
   is ignored until INDELible sees a star followed by a forward slash later on.
*/     

[TYPE] NUCLEOTIDE 1	//  EVERY control file must begin with a [TYPE] command.
			//  The word can be NUCLEOTIDE, AMINOACID or CODON depending 
			//  on what kind of simulation you want to do but must be in 
			//  upper case. The number can be 1 or 2 and chooses the 
			//  algorithm that INDELible uses (see manuscript). Both give 
			//  identical results but in some cases one is quicker.
			//  Other blocks and commands following this statement
			//  can come in any order you like.

[MODEL]    modelname  	//  Evolutionary models are defined in [MODEL] blocks.
[submodel] JC         	//  Here the substitution model is simply set as JC69.
                      	//  No indel model has been given so no indels will occur. 
  
[TREE] treename  (A:0.1,B:0.1);        //  User trees are defined here

[PARTITIONS] partitionname             //  [PARTITIONS] blocks say which models go with
  [treename modelname 1000]            //  which trees and define the length of the
                                       //  sequence generated at the root (1000 here).

[EVOLVE] partitionname 100 outputname  //  This will generate 100 replicate datasets 
                                       //  from the [PARTITIONS] block named above.

// The true alignment will be output in a file named outputname_TRUE.phy
// The unaligned sequences will be output in a file named outputname.fas


