### the homogeneous K80 model:
mod <- DNAmodel()
### the simplest substitution model:
mod <- DNAmodel("JC69")
### the classical GTR + G4 + I:
mod <- DNAmodel("GTR", ncat = 4, invar = TRUE)
### assuming K80 for the two first codon-positions, and
### JC69 for the third position:
mod <- DNAmodel(c("K80", "JC69"), part.model = c(1, 1, 2))
### the same but adding inter-sites variation (the alpha parameter
### is the same for both partitions):
mod <- DNAmodel(c("K80", "JC69"), part.model = c(1, 1, 2),
ncat = 4)
### Only the alpha parameter of ISV is different between the
### partitions (K80 is assumed with equal Ts/Tv):
mod <- DNAmodel(ncat = c(4, 4), part.gamma = c(1, 1, 2))
### A much more complete model resulting in three
### overall partitions:
mod <- DNAmodel(c("K80", "K80"), part.model = c(rep(1, 600), rep(2, 200)),
ncat = c(4, 4), part.gamma = c(rep(1, 200), rep(2, 600)))
Run the code above in your browser using DataCamp Workspace