INDELible

Tutorial Section

Below are example control files that introduce the different features available in INDELible.

Each example file is annotated with actual commands shown in red.

At the beginning or end of most files there are some explanations of what is in the file.

This tutorial and text versions of all the control files are included in the download package.

There is a lot of overlap with the manual section - which is designed to be a command reference guide that you can dip into when you want to know about one command or block type.

In contrast, this tutorial section includes real control files that gradually introduce new and more complex features in real settings.

If you are new to INDELible then it is recommended to start with the simple examples, then read on if you need to.

Please feel free to send me a message if you have any questions, no matter how big or small!

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Simple Examples:

• This very simple control file will show you the basic format of the INDELible control file for nucleotide simulations.
• This very simple control file will show you the basic format of the INDELible control file for amino-acid simulations.
• This very simple control file will show you the basic format of the INDELible control file for codon simulations.



Evolutionary Models:

• This control file will show you how to specify different nucleotide substitution models.
• This control file will show you how to specify different amino-acid substitution models.
• This control file shows how to add gamma rates and/or a proportion of invariable sites.
• This control file shows how to specify codon substitution models & change the genetic code.
• This control file will show you how to specify different codon site models.
• This control file will show you how to specify different indel models.



Non-Homogenous Non-Stationary Models:

• This control file will introduce you to letting models change across the tree, by showing you how to implement codon branch models where ω can vary across the tree.
• This control file will show you how to implement codon branch-site models.
• This control file will go one step further and show you how any aspect of a codon model can vary across the tree, including kappa, omega, the rates of insertion and deletion, and the insertion and deletion length distributions.
• This control file will show you how to implement changing models for nucleotide/amino-acid simulations, including changing stationary frequencies, substitution rates, levels of rate heterogeneity, indel rates and indel distributions.
• This control file will show you how to generate multi-partitioned datasets



Miscellaneous other examples

• This control file will show you how to generate different kinds of trees.
• This control file will show you how to change a number of non-essential settings such as seeds for the random number generator, output file formats, including paup blocks etc..