//                                                                                 //
//  INDELible V1.03 control file - basicnucleotide.txt                             //
//                                                                                 //
//      A basic introduction to the structure of the INDELible 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 number after "NUCLEOTIDE" 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.
  [indelmodel]   NB  0.4 1  //  Geometric indel length distribution (q=0.4, r=1)
  [insertrate]   0.08       //  insertion rate = 0.08 relative to substitution rate of 1
  [deleterate]   0.12       //  deletion rate = 0.12 relative to substitution rate of 1
[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
// To learn how to implement more complicated simulations (or different 
// models) please consult the manual or the other example control files.

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