# DNAmodel

##### 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`

.

##### See Also

##### 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)*