DNAmodel

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.

See Also

mlphylo, dist.dna

Aliases
  • 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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