...
species_network | The species network topology of the data. Branch lengths are not needed. | mandatory |
-gtr | Changes the mutation model from the default JC to GTR. | optional |
-allelemap taxaMap | Species network taxa association. | optional |
| -iterations numIterations | The number of hill climbing iterations to use for each run. | optional |
| -threads numThreads | The number of threads to use when processing. | optional |
| -numberofruns numRuns | The number of times to restart the hill climbing process. | optional |
-noplots | Stop showing plots when finished. | optional |
| -outputdirectory outputLocation | The directory to store the output of the run. | optional |
...