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

Single sequence in an alignment.

Inputs:

totalcount, taxon, value, uncertain

 

totalcount
type: java.lang.Integer
number of states or the number of lineages for this species in SNAPP analysis
Optional input

 

taxon
type: java.lang.String
name of this species
Required input

 

value
type: java.lang.String
sequence data, either encoded as a string or as comma separated list of integers, or comma separated likelihoods/probabilities for each site if uncertain=true.In either case, whitespace is ignored.
Required input

 

uncertain
type: java.lang.Boolean
if true, sequence is provided as comma separated probabilities for each character, with sites separated by a semi-colons. In this formulation, gaps are coded as 1/K,...,1/K, where K is the number of states in the model.
Optional input