sim_twal_with_lns_nsm: Adapter function to simulate the twin alignment using the...

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

Adapter function to simulate the twin alignment using the lns site model

Description

Adapter function to simulate the twin alignment using the lns site model

Usage

sim_twal_with_lns_nsm(
  twin_phylogeny,
  true_alignment = "irrelevant",
  root_sequence,
  subst_matrix = rep(1, 6),
  branch_mutation_rate = 1,
  node_mutation_rate = 1,
  base_frequencies = rep(0.25, 4),
  node_time = 0.001
)

Arguments

twin_phylogeny	a phylogeny of class phylo
true_alignment	a DNA alignment, of class DNAbin
root_sequence	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.
subst_matrix	nucleotide substitution matrix
branch_mutation_rate	mutation rate along the branch. See, among others, sim_unlinked for more details
node_mutation_rate	mutation rate on the node. See, among others, sim_unlinked for more details
base_frequencies	the four base frequencies (a, c, g, t) to be specified to create the rate matrix (i.e. Q matrix) used to simulate alignments
node_time	amount of time spent at the nodes. See, among others, sim_unlinked for more details

Value

an alignment of type DNAbin

Author(s)

Richèl J.C. Bilderbeek

See Also

Use sim_twal_with_uns_nsm to simulate using an unlinked node substitution model. Use sim_tral_with_lns_nsm to simulate a true alignment.

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.