---
name: "indelible"
section: "1"
platform: "linux"
package: "indelible"
version: "1.03-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/indelible"
---

# indelible(1)

powerful and flexible simulator of biological evolution

## NAME

indelible - powerful and flexible simulator of biological evolution

## SYNOPSIS

**indelible**

- No options can be passed via the commandline.

  ## DESCRIPTION

- **indelible** can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. All common evolutionary models are supported.

  - The full documentation for **indelible** is available under */usr/share/doc/indelible/help/index.html*.

  ## CONFIGURATION

- **indelible** reads the settings for a simulation run from a file named *control.txt* in the current directory. The file is split into blocks, with each block controlling one particular aspect of the simulation. Blocks may contain further sub-blocks. Comments can be given in C or C++ style. If **indelible** is executed without a control file present, an example file is generated.

  - **\[TYPE\]** type

  Every control file must begin with a **TYPE** block. The possible types are *NUCLEOTIDE*, *AMINOACID*, and *CODON*.

- **\[SETTINGS\]**

  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.

- **\[MODEL\]** modelname

  This block starts a new evolutionary model to be used for simulation. The particular parameters including substitution models, indel-rates and codon-site models are controlled via submodels. *modelname* can be any name of your choosing.

- **\[TREE\]** treename newick

  This block is used to specify a guide-tree with the given name *treename*. Evolutionary distances are represented as branch lengths for the tree in *NEWICK* format.

- **\[BRANCHES\]**

  These blocks are used to simulate non-stationary and non-homogenous processes. Different models can be specified on different branches of the guide-tree allowing branches to have different models of substitution, indel length distribution, rate heterogeneity, base composition etc.

- **\[PARTITIONS\]** partitionname

  During each run multiple sequence partitions can be simulated. For each partition the guide-tree, evolutionary model and sequence length has to be specified.

- **\[EVOLVE\]**

  Within this block multiple replicas of a partition may be generated.

## COPYRIGHT

Copyright © 2010 William Fletcher License GPLv3+: GNU GPL version 3 or later.\
 This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at \<http://gnu.org/licenses/gpl.html\>.

## ACKNOWLEDGMENTS

William Fletcher and Ziheng Yang (2009). INDELible: A Flexible Simulator of Biological Sequence Evolution, *Molecular Biology and Evolution,* 26(8):1879-1888.

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