BEASTObject that performs calculations based on the State.
A node that can be part of the state.
Unordered set mapping keys to values
Generic class for associating data to tips of a tree, e.g. an Alignment.
Class representing alignment data
An alignment containing sequences randomly generated using agiven site model down a given tree.
Logable: yes, this can be used in a log.
data, tree, siteModel, branchRateModel, sequencelength, outputFileName, sequence, statecount, dataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, taxa, userDataType, *, estimate
| type: beast.base.evolution.alignment.Alignment |
| alignment data which specifies datatype and taxa of the beast.tree |
| Required input |
| type: beast.base.evolution.tree.Tree |
| phylogenetic beast.tree with sequence data in the leafs |
| Required input |
| type: beast.base.evolution.sitemodel.SiteModelInterface$Base |
| site model for leafs in the beast.tree |
| Required input |
| type: beast.base.evolution.branchratemodel.BranchRateModel$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.base.evolution.alignment.Sequence*** |
| sequence and meta data for particular taxon |
| 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: 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: beast.base.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: beast.base.evolution.datatype.DataType$Base |
| non-standard, user specified data type, if specified 'dataType' is ignored |
| Optional input |
| type: java.lang.String |
| Input containing the map |
| Optional input |
| type: java.lang.Boolean |
| whether to estimate this item or keep constant to its initial value |
| Optional input. Default: true |