Description
Uses a hidden markov to assign a species tree to each loci in data coming from a species network.
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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 |
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