    /////////////////////////////////////////////////////////////////////////////////////
    //                                                                                 //
    //  INDELible V1.03 control file - basic.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 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