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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 threetaxon 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, 2.5e8.  mandatory 
rho recombinationRate  The recombination rate in unit of expected number of recombinations per site per generation. For example, 1.5e8.  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 crossover 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 subbranches 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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