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.

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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

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[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.

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[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 10 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.

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[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.

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[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.

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[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.

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[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.

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[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.

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[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.

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[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.

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[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.

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[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.