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
A more flexible alignment simulator. Doesn't require pre-specification of number of taxa.
Logable: yes, this can be used in a log.
tree, siteModel, sequenceLength, outputFileName, startingSequence, startingSequenceAge, sequence, statecount, dataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, taxa, userDataType, *, estimate
| type: beast.base.evolution.tree.Tree |
| Tree down which to simulate sequence evolution. |
| Required input |
| type: beast.base.evolution.sitemodel.SiteModel |
| Site model to use in simulation. |
| Required input |
| type: java.lang.Integer |
| Length of sequence to simulate. |
| Required input |
| type: java.lang.String |
| Name of file (if any) simulated alignment should be saved to. |
| Optional input |
| type: beast.base.evolution.alignment.Sequence |
| Initial sequence to start from. (Default is random draw from equilibrium distribution.) |
| Optional input |
| type: beast.base.core.Function |
| When startingSequence is specified, age (relative to the final sample) at which the sequence simulation starts from. (Default is the age of the root of the tree, but use this to make the starting sequence correspond toan earlier time.) Must be greater than the tMRCA of the tree. |
| 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 |