View source: R/sim_alignment_with_std_nsm_from_params.R
sim_alignment_with_std_nsm_from_params | R Documentation |
Create an alignment with a standard site model
sim_alignment_with_std_nsm_from_params(phylogeny, alignment_params)
phylogeny |
a phylogeny of class phylo |
alignment_params |
parameters to simulate an alignment, as can be created by create_alignment_params |
an alignment of type DNAbin
Richèl J.C. Bilderbeek
use sim_alignment_with_std_nsm to simulate an alignment directlt from a mutation rate, root sequence and site model
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)
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