This allows you to use seq-gen to simulate finite sites mutation models.
When using seq-gen, coala will simulate ancestral tress using the other
simulators, and call seq-gen to simulate finite sites mutations using the
trees. Seq-gen has a low priority, but will always be used when finite
sites mutation models are used.
Usage
activate_seqgen(binary = NULL, priority = 100)
Arguments
binary
The path of the seqgen binary that will be used
for simulations. If none is provided, coala will look for a
binary called 'seqgen' or 'seq-gen' using the PATH variable.
priority
The priority for this simulator. If multiple simulators
can simulate a model, the one with the highest priority will be used.
Installation
You need to download the program from
http://tree.bio.ed.ac.uk/software/seqgen/
and compile the binary prior to invoking this function.
On Debian-based systems, you can alternatively install the package
'seg-gen'.
References
Andrew Rambaut and Nicholas C. Grassly.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence
evolution along phylogenetic trees.
Comput Appl Biosci (1997) 13 (3): 235-238
doi:10.1093/bioinformatics/13.3.235
See Also
Other simulators:
simulator_ms,
simulator_msms,
simulator_scrm