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).
The "*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.
alignathonBurninFiles.tar.gz (625 MB)
md5sum: 404ca680efc0d23384f542c75688ac86
The files in the provided archive were used to perform the primate simulation. Details are included in the xml.
alignathonMRCAFiles.tar.gz (829 MB)
md5sum: 02d2bc60af0a644257812baf6d7aae92
The files in the provided archive were used to perform the mammal simulation. Details are included in the xml.
alignathonMRCAFiles.tar.gz (829 MB)
md5sum: 02d2bc60af0a644257812baf6d7aae92
The files in the provided archive were used to perform the burnin for the test set. Details are included in the xml.
alignathonTestBurninFiles.tar.gz (9.5 MB)
md5sum: bced89fd4e10ef83b56b5dbbe1b2337c
The files in the provided archive were used to perform the test set simulation. Details are included in the xml.
alignathonTestMRCAFiles.tar.gz (51 MB)
md5sum: 274b1566ff7c29a45fca7a04911e54f6