implemented by the following |
beast.app.seqgen.SimulatedAlignment |
beast.evolution.alignment.AscertainedAlignment |
beast.evolution.alignment.FilteredAlignment |
BEASTObject that performs calculations based on the State.
Unordered set mapping keys to values
Class representing alignment data
sequence, taxa, statecount, dataType, userDataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, *
 
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 |