    /////////////////////////////////////////////////////////////////////////////////////
    //                                                                                 //
    //  INDELible V1.03 control file - settings.txt                                    //
    //                                                                                 //
    //      How to include paup blocks, set seeds for the random number generator,     //
    //      change the output format for generated data, or how to print "reports"     //
    //                                                                                 //
    /////////////////////////////////////////////////////////////////////////////////////

    [TYPE] NUCLEOTIDE 2	//  nucleotide simulation using algorithm from method 2

      //
      // * If a command is not specified in the [SETTINGS] block then it will have the
      //   default value shown below. The only exception to this is [randomseed] whose
      //   value will be randomly chosen if not specified.
      // * If no [SETTINGS] block is specified all commands will have these default values.
      // * More information on each of the commands can be found at the end of the file.
      //

    [SETTINGS]
      [ancestralprint]           FALSE     // NEW, SAME or FALSE
      [output]                   PHYLIP    // FASTA, NEXUS, PHYLIP or PHYLIPT
      [phylipextension]          phy       // any alpha-numeric string
      [nexusextension]           nex       // any alpha-numeric string
      [fastaextension]           fas       // any alpha-numeric string
      [randomseed]               1568746   // any integer
      [printrates]               FALSE     // FALSE or TRUE
      [insertaslowercase]        TRUE      // FALSE or TRUE
      [markdeletedinsertions]    FALSE     // FALSE or TRUE
      [printcodonsasaminoacids]  FALSE     // FALSE or TRUE
      [fileperrep]               FALSE     // FALSE or TRUE

    [MODEL] mymodel  [submodel]  JC

    [TREE] t1 ((A:0.1,B:0.1):0.1,(C:0.1,D:0.1):0.1);

    [PARTITIONS] Pname  [t1 mymodel 1000]   // tree t1, model mymodel, root length 1000

    [EVOLVE]     Pname  10  filename        // 10 replicates generated from partition Pname

    /*
      [ancestralprint]
      * NEW will print ancestral sequences in a separate file to leaf sequences.
      * SAME prints ancestral sequences in the same file as the leaf sequences.
      * FALSE will not print any ancestral sequences.
      * It should be noted that if you used different guide trees for different partitions
        in a partitioned (multi-gene) analysis then only the root sequence will be printed
        in the SAME/NEW file specified in this command.

      [output]
      * Unaligned sequences are always output in FASTA format as e.g. filename.fas
      * This command sets the output type for the true alignment and prints it to a file
        named e.g. filename_TRUE.phy
      * FASTA, NEXUS, PHYLIP will print out sequences to file in either
        fasta, nexus, or phylip format respectively.
      * FASTA is used by NCBI and accepted by most sequence alignment programs.
        NEXUS is used by e.g. MacClade, Mesquite, ModelTest, MrBayes and PAUP*.
        PHYLIP is used by PHYLIP and PAML.
      * PHYLIPT gives PHYLIP format with filenames truncated to 8 characters.

      [phylipextension]
      * This command sets the file extension for true alignments in phylip format so they
        are e.g. filename.phy or whatever you choose them to be.

      [nexusextension]
      * This command sets the file extension for true alignments in nexus format so they
        are e.g. filename.nex or whatever you choose them to be.

      [fastaextension]
      * This command sets the file extension for fasta formatted output files so they
        are e.g. filename.fas or whatever you choose them to be.

      [randomseed]
      * This must be an integer value and is used to seed the random number generator.
      * Running simulations with the same random seed value (and the same control file)
        will produce identical datasets.

      [printrates]
      * TRUE will print out a detailed output file for each replicate of each block
        that lists what the site-classes or relative rates of substitution are.
      * FALSE will not print any rates information.
      * Follow these links for examples of the output for NUCLEOTIDE / AMINOACID simulations,
        or for CODON simulations.

      [markdeletedinsertions]
      * TRUE will output inserted bases/residues that have been subsequently been
        deleted as * rather than - for easy identification.
      * FALSE leave everything as -.

      [insertaslowercase]
      * TRUE will output inserted bases/residues as lower case letters for easy identification.
      * FALSE will output all bases/residues as upper case letters.

      [printcodonsasaminoacids]
      * TRUE will output codon datasets as amino-acids - how they are translated will
        depend on the genetic code specified in the model.
      * FALSE will print codons as nucleotide triplets.

      [fileperrep]
      * TRUE will output each replicate dataset in a separate file.
        Unaligned sequences will go in e.g. filename_1.fas, filename_2.fas, etc
        The true alignment will go in e.g. filename_TRUE_1.phy, filename_TRUE_2.phy, etc
      * FALSE will print all replicates in a single file.
        Unaligned sequences for each dataset will all go in e.g. filename.fas
        All the true alignments will go in e.g. filename_TRUE.phy
      * If a file called paupstart.txt (or paupend.txt) exists in the same directory as
        INDELible then it will be copied to the beginning (or end) of each file.
      * If a file called paupmiddle.txt exists in the same directory as INDELible then it
        will be copied to e.g. filename_TRUE.phy after each replicate datset.
      * These features are useful if you want to include PAUP or MrBayes blocks in your files.
    */