BEAST v2.5.0 Documentation: beast.app.seqgen.SequenceSimulator

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.

Inputs:

data, tree, siteModel, branchRateModel, sequencelength, outputFileName, merge, iterations

 

data
type: beast.evolution.alignment.Alignment
alignment data which specifies datatype and taxa of the beast.tree
Required input

 

tree
type: beast.evolution.tree.Tree
phylogenetic beast.tree with sequence data in the leafs
Required input

 

siteModel
type: beast.evolution.sitemodel.SiteModelInterface$Base
site model for leafs in the beast.tree
Required input

 

branchRateModel
type: beast.evolution.branchratemodel.BranchRateModel$Base
A model describing the rates on the branches of the beast.tree.
Optional input

 

sequencelength
type: java.lang.Integer
nr of samples to generate (default 1000).
Optional input. Default: 1000

 

outputFileName
type: java.lang.String
If provided, simulated alignment is written to this file rather than to standard out.
Optional input

 

merge
type: beast.app.seqgen.MergeDataWith***
specifies template used to merge the generated alignment with
Optional input

 

iterations
type: java.lang.Integer
number of times the data is generated
Optional input. Default: 1