indelible1

Usage

Overview

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.

Acknowledgments

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