Defines Models of DNA Evolution
This function defines a model of evolution for a set of DNA sequences with possible partitions.
DNAmodel(model = "K80", partition = 1, ncat.isv = 1, invar = FALSE, equal.isv = TRUE, equal.invar = 1)
- a vector of mode character giving the substition model.
- a vector of integers defining the partitions for the substition models (eventually recycled).
- the number of categories in each partition.
- a logical value specifying whether there are invariants.
- a logical value specifying whether the `alpha'
parameter is the same in all partitions; has no effet if
ncat = 1or if
partition = 1.
- similar to the argument above but for the proportion of invariants.
partition is recycled along the sequence: thus by default there
is a single partition. For instance, to partition a sequence of 1000
sites into two partitions of equal length, one will use
partition = c(rep(1, 500), rep(2, 500)). The partitions must be
numbered with a series of integers (1, 2, 3, ...). To partition the
codon positions, one could do
partition = c(1, 1, 2).
The substition models are the same in all partitions. Branch lengths are the same in all partitions up to a multiplying coefficient (the contrast parameter, denoted 'xi').
The substitution models must be among the followings:
"GTR". These models (except
HKY85 and GTR) are described in the help page of
Inter-sites variation in substitution rates (ISV) is allowed by
ncat.isv greater than one.
- an object of class
"DNAmodel"with components defined by the arguments of the function call.
The result of this function is not intended to be used by the user,
but rather to be passed to
### the K80 model: mod <- DNAmodel() ### the simplest substitution model: mod <- DNAmodel("JC69") ### the classical GTR + G4 + I: mod <- DNAmodel("GTR", ncat.isv = 4, invar = TRUE) ### codon-partitioning (with K80): mod <- DNAmodel(partition = c(1, 1, 2)) ### the same but adding inter-sites variation (the alpha parameter ### is the same for both partitions): mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4) ### ... and with different `alpha' for each partition: mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4, equal.isv = FALSE)