/////////////////////////////////////////////////////////////////////////////////////
//                                                                                 //
//  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]    
  [randomseed]               1568746   // seed for random generator so outputs can be checked
  [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 20]   // tree t1, model mymodel, root length 20

 
[EVOLVE]     Pname  5  filename        // 5 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.
*/