ape (version 1.8-1)

DNAmodel: Defines Models of DNA Evolution

Description

This function defines a model of evolution for a set of DNA sequences with possible partitions.

Usage

DNAmodel(model = "K80", part.model = 1,
         ncat = 1, part.gamma = 1,
         invar = FALSE, part.invar = 1)

Arguments

model

a vector of mode character giving the substition model for each partition (must be of the same length than unique(part.model)).

part.model

a vector of integers defining the partitions for the substition models (eventually recycled).

ncat

the number of categories in each partition defined by part.gamma (must be of the same length than unique(part.gamma)).

part.gamma

a vector of integers defining the partitions for the inter-sites variation in substitution parameters (eventually recycled).

invar

a vector of logical values specifying whether there are invaraints in each partition defined by part.invar (must be of the same length than unique(part.invar)).

part.invar

a vector of integers defining the partitions for the proportion of invariants (eventually recycled).

Value

• an object of class "DNAmodel" with components defined by the arguments of the function call.

Details

The six arguments of this function work in pairs: model defines the substitution model for each partition defined by part.model. The latter 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 part.model = 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 part.model = c(1, 1, 2).

There must be as many models than partitions, but the former may be the same. For instance, model = c("K80", "K80") means that partitions 1 and 2 evolve under Kimura's model but its parameters will be estimated separately in each partition. In addition, 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: "JC69" "K80", "F81", "K84", "HKY85", "T92", "TN93", and "GTR". These models (except HKY85 and GTR) are described in the help page of dist.dna.

The two other pairs of functions work in the same way. This decoupling allows one to share some parameters accross partitions (see examples).

See Also

mlphylo, dist.dna

Examples

### 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)))