To generate simulated data as described in "A case for the ancient origin of coronaviruses" follow these steps
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Download and install HyPhy (www.hyphy.org). You will need version 2.13 or later, which may only be available as a source download. You can always obtain the latest versions of HyPhy from https://github.com/veg/hyphy
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Run BS-REL_simulator.bf through HyPhy, e.g.
$HYPHYMP ./BS-REL_simulator.bf -
When propmted,
- supply the name of the file containing model fit information of the RdRp gene (rdrp.fit)
- indicate the total desired tree length (expected substitutions per nucleotide/site)
- choose the number of replicates to be generated
- provide the file system path to save the replicates to