Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc.
Performs random sequence generation for a given site model. Sequences for the leave nodes in the tree are returned as an alignment.
data, tree, siteModel, branchRateModel, sequencelength, outputFileName, merge, iterations
 
type: beast.evolution.alignment.Alignment |
alignment data which specifies datatype and taxa of the beast.tree |
Required input |
 
type: beast.evolution.tree.Tree |
phylogenetic beast.tree with sequence data in the leafs |
Required input |
 
type: beast.evolution.sitemodel.SiteModelInterface$Base |
site model for leafs in the beast.tree |
Required input |
 
type: beast.evolution.branchratemodel.BranchRateModel$Base |
A model describing the rates on the branches of the beast.tree. |
Optional input |
 
type: java.lang.Integer |
nr of samples to generate (default 1000). |
Optional input. Default: 1000 |
 
type: java.lang.String |
If provided, simulated alignment is written to this file rather than to standard out. |
Optional input |
 
type: beast.app.seqgen.MergeDataWith*** |
specifies template used to merge the generated alignment with |
Optional input |
 
type: java.lang.Integer |
number of times the data is generated |
Optional input. Default: 1 |