Create testing parameters for the alignment simulation.
create_test_alignment_params(
sim_tral_fun = pirouette::sim_tral_with_std_nsm,
root_sequence = "acgt",
rng_seed = 0,
fasta_filename = pirouette::get_temp_fasta_filename()
)a list of alignment parameters alignment_params <- create_test_alignment_params() check_alignment_params(alignment_params)
function to simulate a
true alignment with.
This function must have two arguments,
called true_phylogeny (which will hold the true phylogeny)
and root_sequence (which holds the DNA root sequence).
The return type must be DNAbin.
Use check_sim_tral_fun to verify if the function has the right signature and output.
Some standard functions:
Use get_sim_tral_with_std_nsm_fun to get a function (sim_tral_with_std_nsm) the use a standard site model.
Use get_sim_tral_with_lns_nsm_fun to get a function (sim_tral_with_lns_nsm) the use a linked node substitution site model.
Use get_sim_tral_with_uns_nsm_fun to get a function (sim_tral_with_uns_nsm) the use an unlinked node substitution site model.
the DNA sequence at the root of the phylogeny. By default, this will consist out of an equal amount of each letter Use check_root_sequence to check if a root sequence is valid.
a random number generator seed
name of a FASTA file. Use get_alignment_id to get the ID of the alignment
Richèl J.C. Bilderbeek