# 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 & more complex features in real settings.
- If you are new to INDELible then it is recommended to read the examples in order.

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 will show you how to add gamma rates and/or a proportion of invariable sites.
- This control file will show you 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 site-branch 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 etc..