# DNAmodel

From ape v2.1-1
0th

Percentile

##### Defines Models of DNA Evolution

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

Keywords
models
##### Usage
DNAmodel(model = "K80", partition = 1,
ncat.isv = 1, invar = FALSE,
equal.isv = TRUE, equal.invar = 1)
##### Arguments
model
a vector of mode character giving the substition model.
partition
a vector of integers defining the partitions for the substition models (eventually recycled).
ncat.isv
the number of categories in each partition.
invar
a logical value specifying whether there are invariants.
equal.isv
a logical value specifying whether the alpha' parameter is the same in all partitions; has no effet if ncat = 1 or if partition = 1.
equal.invar
similar to the argument above but for the proportion of invariants.
##### Details

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: "JC69" "K80", "F81", "F84", "HKY85", "T92", "TN93", and "GTR". These models (except HKY85 and GTR) are described in the help page of dist.dna.

Inter-sites variation in substitution rates (ISV) is allowed by specifying ncat.isv greater than one.

##### Value

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

##### Note

The result of this function is not intended to be used by the user, but rather to be passed to mlphylo.

mlphylo, dist.dna

• DNAmodel
##### Examples
### 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)
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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