Rev Language Reference



dnPhyloCTMCDASequence(Tree tree, RateGeneratorSequence Q, CladogeneticProbabilityMatrix cladoProbs, Simplex rootFrequencies, RealPos branchRates, RealPos[] siteRates, Probability pInv, Natural nSites, String type, Bool storeInternalNodes, Bool treatAmbiguousAsGap, String coding)


tree : Tree (pass by const reference)
The tree along which the process evolves.
Q : RateGeneratorSequence (pass by const reference)
The global or branch-specific rate matrices.
cladoProbs : CladogeneticProbabilityMatrix (pass by const reference)
Default : NULL
rootFrequencies : Simplex (pass by const reference)
The root specific frequencies of the characters, if applicable.
Default : NULL
branchRates : RealPos (pass by const reference)
The global or branch-specific rate multipliers.
Default : 1
siteRates : RealPos[] (pass by const reference)
The rate categories for the sites.
Default : [ ]
pInv : Probability (pass by const reference)
The probability of a site being invariant.
Default : 0
nSites : Natural (pass by value)
The number of sites, used for simulation.
Default : 10
type : String (pass by value)
The data type, used for simulation and initialization.
Default : DNA
Options : DNA|RNA|AA|PoMo|Protein|Standard|NaturalNumbers|Restriction
storeInternalNodes : Bool (pass by value)
Should we store internal node states in the character matrix?
Default : FALSE
treatAmbiguousAsGap : Bool (pass by value)
Should we treat ambiguous characters as gaps/missing?
Default : FALSE
coding : String (pass by value)
Default : all

Domain Type