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| Starting State Settings | ||
| -st startingTree | Specify the starting tree topology and node heights. The input tree should be ultrametric with branch lengths in units of generations. For example, ((H:160000, C:160000):60000, G:220000); species a three-taxon tree with an internal node height of 160,000 generations and root node height of 220,000 generations. See the example below. | mandatory |
-mu mutationRate | The mutation rate in unit of expected number of mutations per site per generation. For example, 2.5e-8. | mandatory |
| -rho recombinationRate | The recombination rate in unit of expected number of recombinations per site per generation. For example, 1.5e-8. | mandatory |
-nhsigma nodeHeightInitialSigma | The starting standard deviation of the variational posterior of each node height. The default value is 20,000. | optional |
| -pssigma popSizeInitialSigma | The starting standard deviation of the variational posterior of each population size. The default value is 10,000. | optional |
| Prior Settings | ||
| -psp popSizePrior | Mean value of the prior of population sizes. The default value is 50,000. | optional |
| Likelihood Simulator Settings | ||
| -n0 N0ForMS | N0 for | optional |
| -r crossoverRate | The cross-over rate that determines the length of simulation for building coalHMM. For details see ms documentation ("Crossing over") and our paper. Can use 1,000 as a starting point. | mandatory |
| -nb numSubBranch | The number of sub-branches on each internal branch of the species tree for refining coalHMM state space. For details see our paper. Can use 2 as a starting point. | mandatory |
| BBVI Settings | ||
| -ns samplePerIter | The number of samples per iteration of BBVI for estimating gradient. The default value is 50. | optional |
| -niter numIter | The number of iterations of BBVI. The default value is 200. | optional |
| -nhmeanlr nodeHeightMeanLearningRate | Learning rate for the mean parameter of the variational posterior of node heights. The default value is 20,000. | optional |
| -psmeanlr popSizeMeanLearningRate | Learning rate for the mean parameter of the variational posterior of population sizes. The default value is 10,000. | optional |
| -nhsigmalr nodeHeightSigmaLearningRate | Learning rate for the standard deviation parameter of the variational posterior of node heights. The default value is 500. | optional |
| -pssigmalr popSizeSigmaLearningRate | Learning rate for the standard deviation parameter of the variational posterior of population sizes. The default value is 500. | optional |
| -nhsigmamin nodeHeigthSigmaMinimum | The minimum value of the standard deviation of node heights variational posterior. Since BBVI is possible to reach a negative standard deviation if the learning rate is not set carefully, a minimum value is required so that the standard deviation would not drop below the specified value during BBVI searches. The default value is 10,000. | optional |
| -pssigmamin popSizeSigmaMinimum | The minimum value of the standard deviation of population sizes variational posterior. The default value is 3,000. | optional |
Example
Download: test test.nex
#NEXUS H TCGCTGTCTCATACTATATGGAGAGTCAAGGGGGTTGAGATAATTGTCGCATTGTCTAAGTGAATGGCGTAAAGCGAAC....... BEGIN TREES; BEGIN PHYLONET; |
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