pirouette (version 1.6.9)

get_sim_tral_with_std_nsm_fun: Get a function to simulate the true alignment with, that uses a standard site model.

Description

Get a function to simulate the true alignment with, that uses a standard site model.

Usage

get_sim_tral_with_std_nsm_fun(
  mutation_rate = 1,
  site_model = beautier::create_jc69_site_model()
)

Value

a function

Arguments

mutation_rate

the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid.

site_model

a nucleotide substitution model, which can be:

• A standard nucloetide substitution model, as created by create_site_model

• lns: a linked node-substitution model

• uns: an unlinked node-substitution model

Examples

f <- get_sim_tral_with_std_nsm_fun(
  mutation_rate = 0.1
)
check_sim_tral_fun(f)

alignment_params <- create_test_alignment_params(
  sim_tral_fun = f,
  root_sequence = "acgt",
)
true_alignment <- sim_true_alignment(
  true_phylogeny = ape::read.tree(text = "((A:1, B:1):1, C:2);"),
  alignment_params = alignment_params
)