# INDELible

## [SETTINGS] block

- This block specifies non-essential user preferences such as output file types and formats, seeds for the random number generator, and whether to output detailed reports.
- If a command is not specified in the [SETTINGS] block then it will have the default value shown below in the example usage. 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.
- Please click on any of the commands to learn more about them.

Example Usage:

    [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

    [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 SAME/NEW file specified in the last command.
- Return to example usage.

    [output]

- 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.
- 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
- For more details about different output files see the examples section.
- Return to example usage.

    [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.
- Return to example usage.

    [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.
- Return to example usage.

    [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.
- Return to example usage.

    [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.
- Return to example usage.

    [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.
- Return to example usage.

    [markdeletedinsertions]

- TRUE will output inserted bases/residues that have been subsequently been deleted as * rather than - for easy identification.
- FALSE will output all deletions as "-".
- Return to example usage.

    [insertaslowercase]

- TRUE will output inserted bases/residues in lower case letters for easy identification.
- FALSE will output all bases/residues as upper case letters.
- Return to example usage.

    [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.
- Return to example usage.

    [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 output 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.
- Return to example usage.