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| Parametrization setting | ||
| -bl | Infer branch length of the branches in the species tree, instead of node heights of internal nodes. This option can reduce sampling illegal tree configurations when estimating the gradient of the ELBO by Monte Carlo samples. | optional |
| 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. (Only used when -bl is not set.) | optional |
| -pssigma popSizeInitialSigma | The starting standard deviation of the variational posterior of each population size. The default value is 10,000. | optional |
| -blsigma branchLengthInitialSigma | The starting standard deviation of the variational posterior of each branch length. The default value is 20,000. (Only used when -bl is set.) | 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 |
| -len simulationShortRegionLength | Simulating multiple independent short regions when building the HMM could save time compared to simulating a long region. This parameter is the length of each independent short region simulation. The default value is 5,000. | optional |
| 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. (Only used when -bl is not set.) | optional |
| -psmeanlr popSizeMeanLearningRate | Learning rate for the mean parameter of the variational posterior of population sizes. The default value is 10,000. | optional |
| -blmeanlr branchLengthMeanLearningRate | Learning rate for the mean parameter of the variational posterior of branch lengths. The default value is 20,000. (Only used when -bl is set.) | optional |
| -nhsigmalr nodeHeightSigmaLearningRate | Learning rate for the standard deviation parameter of the variational posterior of node heights. The default value is 500. (Only used when -bl is not set.) | optional |
| -pssigmalr popSizeSigmaLearningRate | Learning rate for the standard deviation parameter of the variational posterior of population sizes. The default value is 500. | optional |
| -blsigmalr branchLengthSigmaLearningRate | Learning rate for the standard deviation parameter of the variational posterior of branch lengths. The default value is 500. (Only used when -bl is set.) | 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. (Only used when -bl is not set.) | optional |
| -pssigmamin popSizeSigmaMinimum | The minimum value of the standard deviation of population sizes variational posterior. The default value is 3,000. | optional |
| -blsigmamin branchLengthSigmaMinimum | The minimum value of the standard deviation of branch length variational posterior. The default value is 10,000. (Only used when -bl is set.) | optional |
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