BEASTObject that performs calculations based on the State.
Unordered set mapping keys to values
Class representing alignment data
An alignment containing sequences randomly generated using agiven site model down a given tree.
data, tree, siteModel, branchRateModel, sequencelength, outputFileName, sequence, taxa, statecount, dataType, userDataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, *
 
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 additionally written to this file. |
Optional input |
 
type: beast.evolution.alignment.Sequence*** |
sequence and meta data for particular taxon |
Optional input |
 
type: beast.evolution.alignment.TaxonSet |
An optional taxon-set used only to sort the sequences into the same order as they appear in the taxon-set. |
Optional input |
 
type: java.lang.Integer |
maximum number of states in all sequences |
Optional input |
 
type: java.lang.String |
data type, one of {aminoacid=aminoacid, binary=binary, integer=integer, nucleotide=nucleotide, standard=standard, twoStateCovarion=twoStateCovarion, user defined=user defined} |
Optional input. Default: nucleotide |
 
type: beast.evolution.datatype.DataType$Base |
non-standard, user specified data type, if specified 'dataType' is ignored |
Optional input |
 
type: java.lang.Boolean |
sets weight to zero for sites that are invariant (e.g. all 1, all A or all unkown) |
Optional input. Default: false |
 
type: java.lang.String |
comma separated list of weights, one for each site in the sequences. If not specified, each site has weight 1 |
Optional input |
 
type: java.lang.Boolean |
is true if the alignment allows ascertainment correction, i.e., conditioning the Felsenstein likelihood on excluding constant sites from the alignment |
Optional input. Default: false |
 
type: java.lang.Integer |
first site to condition on, default 0 |
Optional input. Default: 0 |
 
type: java.lang.Integer |
last site to condition on (but excluding this site), default 0 |
Optional input. Default: 0 |
 
type: java.lang.Integer |
interval between sites to condition on (default 1) |
Optional input. Default: 1 |
 
type: java.lang.Integer |
first site to condition on, default 0 |
Optional input. Default: 0 |
 
type: java.lang.Integer |
last site to condition on, default 0 |
Optional input. Default: 0 |
 
type: java.lang.Integer |
interval between sites to condition on (default 1) |
Optional input. Default: 1 |
 
type: java.lang.String |
Input containing the map |
Optional input |