View source: R/sim_tral_with_uns_site_model.R
sim_tral_with_uns_nsm | R Documentation |
linked_node_sub
(lns) site model.Adapter function to simulate an alignment
with the linked_node_sub
(lns) site model.
sim_tral_with_uns_nsm(
true_phylogeny,
root_sequence,
branch_subst_matrix = rep(1, 6),
node_subst_matrix = 1,
branch_mutation_rate = 1,
node_mutation_rate = 1,
base_frequencies = rep(0.25, 4),
node_time = 0.001
)
true_phylogeny |
the true phylogeny; the actual evolutionary history of the species, of class phylo |
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. |
branch_subst_matrix |
substitution matrix along the branches. See, among others, sim_unlinked for more details |
node_subst_matrix |
substitution matrix on the nodes. See, among others, sim_unlinked for more details |
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 |
an alignment of type DNAbin
Richèl J.C. Bilderbeek
Use sim_tral_with_lns_nsm to simulate the true alignment with a linked node substitution model. Use sim_twal_with_uns_nsm to simulate the twin alignment with an unlinked node substitution model. Use get_sim_tral_with_uns_nsm_fun to get a partially evaluated unary function.
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