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indelible - powerful and flexible simulator of biological evolution



No options can be passed via the commandline.


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

The full documentation for indelible is available under


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,

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

[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

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.

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


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


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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