Specifies a fixed random seed (used for parsimony inferences AND rapid bootstrapping). This only makes sense if you like to reproduce results (which isn't possible for all cases).
Recommended default setting is (empty). The number of seconds since 'epoch' will be used in that case.
CPU thread override
Specify number of threads to use (for bootstrapping and ML search).
The script tries to detect the number of CPU cores available. If it fails to detect the (correct) number of cores on your machine, you can set the environment variable PBS_NP to the number of cores available.
If the number of threads is not specified (=empty, which is recommended), the script will check the input alignment and automatically select the number of threads to use.
If there are at least twice as many cores as threads wanted (approx.), bootstrapping and ML search will run asynchronously. Otherwise they run one after the other.
When specifying the number of threads manually, make sure you do not specify more threads than cores available on your hardware, otherwise you'll encounter a massive performance penalty!
If you like to force asynchronous execution of bootstrapping and ML search, set thread override to CORES/2 (e.g. if you have 8 cores select 4 threads).
If you like to force sequential execution of bootstrapping and ML search, set the number of cores to a higher value. Please note that selecting too many threads may also result in degraded performance.