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PROGRAM:
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 continous
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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