jaatha (version 2.7.0)

dm.setMutationModel: Defines what mutation model is used for simulations

Description

As default, we simulate mutation using the Infinite Sites Model. Using the function, you can change it either to the Hasegawa, Kishino and Yano (HKY), to the Felsenstein and Churchill 96 (F84) or to the Generalised time reversible (GTR) model. This requires that seq-gen is installed on our system.

Usage

dm.setMutationModel(dm, mutation.model, base.frequencies, tstv.ratio, gtr.rates)

Arguments

dm

The demographic model for which the mutation model will be set.

mutation.model

The mutation model you want to use. Can be HKY, F84 or GTR.

base.frequencies

The equilibrium frequencies of the four bases. Must be a numeric vector of length four. Order is A, C, G, T.

tstv.ratio

The ratio of transitions to transversions. The default is 0.5, which means that all amino acid substitutions are equally likely. In this case, the HKY model is identical to the Felsenstein 81 model.

gtr.rates

The rates for the amino acid substitutions. Must be a numeric vector of length six. Order: A->C, A->G, A->T, C->G, C->T, G->T.

Value

• The demographic model with the new mutation model.

Details

The HKY and F84 models use the the arguments 'base.frequencies' and 'tstv.ratio'. The GTR model uses 'gtr.rates'.

Examples

dm <- dm.createThetaTauModel(10:11, 10, 100)
dm <- dm.addOutgroup(dm, "2*tau")
dm.hky <- dm.setMutationModel(dm, "HKY", c(0.2, 0.2, 0.3, 0.3), 2)
dm.f81 <- dm.setMutationModel(dm, "F84", c(0.3, 0.2, 0.3, 0.2), 2)
dm.gtr <- dm.setMutationModel(dm, "GTR", gtr.rates=c(0.2, 0.2, 0.1, 0.1, 0.1, 0.2))