BEAST v2.5.0 Documentation: beast.evolution.alignment.FilteredAlignment

BEASTObject that performs calculations based on the State.
Unordered set mapping keys to values
Class representing alignment data
Alignment based on a filter operation on another alignment

Inputs:

filter, data, constantSiteWeights, sequence, taxa, statecount, dataType, userDataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, *

 

filter
type: java.lang.String
specifies which of the sites in the input alignment should be selected First site is 1.Filter specs are comma separated, either a singleton, a range [from]-[to] or iteration [from]:[to]:[step]; 1-100 defines a range, 1-100 or 1:100:3 defines every third in range 1-100, 1::3,2::3 removes every third site. Default for range [1]-[last site], default for iterator [1]:[last site]:[1]
Required input

 

data
type: beast.evolution.alignment.Alignment
alignment to be filtered
Required input

 

constantSiteWeights
type: beast.core.parameter.IntegerParameter
if specified, constant sites will be added with weights specified by the input. The dimension and order of weights must match the datatype. For example for nucleotide data, a 4 dimensional parameter with weights for A, C, G and T respectively need to be specified.
Optional input

 

sequence
type: beast.evolution.alignment.Sequence***
sequence and meta data for particular taxon
Optional input

 

taxa
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

 

statecount
type: java.lang.Integer
maximum number of states in all sequences
Optional input

 

dataType
type: java.lang.String
data type, one of [aminoacid, binary, integer, nucleotide, standard, twoStateCovarion, user defined]
Optional input. Default: nucleotide

 

userDataType
type: beast.evolution.datatype.DataType$Base
non-standard, user specified data type, if specified 'dataType' is ignored
Optional input

 

strip
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

 

weights
type: java.lang.String
comma separated list of weights, one for each site in the sequences. If not specified, each site has weight 1
Forbidden: must not be specified

 

ascertained
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

 

excludefrom
type: java.lang.Integer
first site to condition on, default 0
Optional input. Default: 0

 

excludeto
type: java.lang.Integer
last site to condition on (but excluding this site), default 0
Optional input. Default: 0

 

excludeevery
type: java.lang.Integer
interval between sites to condition on (default 1)
Optional input. Default: 1

 

includefrom
type: java.lang.Integer
first site to condition on, default 0
Optional input. Default: 0

 

includeto
type: java.lang.Integer
last site to condition on, default 0
Optional input. Default: 0

 

includeevery
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