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
Objects of this type are regular beast Alignments, but are populated using data read in from an external fasta file. Sequence labels used as taxon labels.
Logable: yes, this can be used in a log.
fileName, url, xmlFileName, endsWith, includeOnly, sequence, statecount, dataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, taxa, userDataType, *, estimate
| type: java.lang.String |
| Name of file containing sequence alignment. |
| Either this, or url needs to be specified |
| type: java.lang.String |
| URL from which to download sequence alignment. |
| Either this, or fileName needs to be specified |
| type: java.lang.String |
| Name of file to write XML fragment to. |
| Optional input |
| type: java.lang.String |
| If provided, include only those sequences whose header strings end with the provided substring. |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| Only include the taxa listed in this taxon set. |
| 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 |