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.
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