For each simulation listed below we have provided the necessary input files and command to run the simulation. For each simulation there are between two and three files to download. The "
simulationInfo*.xml" files are produced by the simulation and contain, among other things, the command that was used to run the simulation in the tag
<command> (note that the value for the
--inputNewick parameter should be contained in quotation marks when actually executing the command).
*Files.tar.gz" archive contains the root cycle (evolver terminology) for the simulation and the parameters directory. If the simulation has a "
*Parameters.tar.gz" archive then the root cycle and parameters directory are simply being stored separately (this is done for the Primates and Mammals simualtions because they use the same root cycle.
The files in the provided archive were used to perform the burnin for both the primate and mammal simulations (despite the primate and mammal simulation xml descriptions refering to different filenames, the files were indeed the same). Details are included in the xml.