indelible - powerful and flexible simulator of biological
evolution
- 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 © 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>.
William Fletcher and Ziheng Yang (2009). INDELible: A Flexible
Simulator of Biological Sequence Evolution, Molecular Biology and
Evolution, 26(8):1879-1888.