pirouette (version 1.6.9)

sim_alignment_with_std_nsm_from_params: Create an alignment with a standard site model

Description

Create an alignment with a standard site model

Usage

sim_alignment_with_std_nsm_from_params(phylogeny, alignment_params)

Value

an alignment of type DNAbin

Arguments

phylogeny

a phylogeny of class phylo

alignment_params

parameters to simulate an alignment, as can be created by create_alignment_params

Author

Richèl J.C. Bilderbeek

See Also

use sim_alignment_with_std_nsm to simulate an alignment directlt from a mutation rate, root sequence and site model

Examples

phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
alignment_params <- create_alignment_params(
  root_sequence = "aaaa",
  sim_tral_fun = get_sim_tral_with_std_nsm_fun(
    mutation_rate = 0.1
  )
)
alignment <- sim_alignment_with_std_nsm_from_params(
  phylogeny = phylogeny,
  alignment_params = alignment_params
)
check_alignment(alignment)