pirouette (version 1.6.9)

sim_alignment_with_n_mutations: Converts a phylogeny to a random DNA alignment

Description

The function is used to create both the true (see create_true_alignment) and twin alignment (see sim_twin_alignment).

Usage

sim_alignment_with_n_mutations(
  phylogeny,
  root_sequence,
  n_mutations,
  mutation_rate = 1,
  site_model = beautier::create_jc69_site_model(),
  max_n_tries = 100,
  verbose = FALSE
)

Value

an alignment

an alignment of type DNAbin

Arguments

phylogeny

a phylogeny 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.

n_mutations

the number of different base pairs between root sequence and the resulting alignment. Set to NA if any number of mutations is fine.

mutation_rate

the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid.

site_model

a nucleotide substitution model, which can be:

• A standard nucloetide substitution model, as created by create_site_model

• lns: a linked node-substitution model

• uns: an unlinked node-substitution model

max_n_tries

number of attempts to simulate a DNA alignment with the desired number of mutations. If this number of attempts is reached, the funcion will show a warning and return the last DNA alignment simulated.

verbose

if TRUE, show more output

Author

Richèl J.C. Bilderbeek, Giovanni Laudanno

Richèl J.C. Bilderbeek

See Also

Use create_tral_file to save the simulated alignment directly to a file.

Use sim_tral_with_std_nsm simulate the true alignment with a standard site model. Use sim_twal_with_std_nsm simulate the twin alignment with a standard site model.

Examples

# Create the phylogeny to simulate the alignment on
n_taxa <- 5
phylogeny <- ape::rcoal(n_taxa)

# Use default settings to create the alignment
alignment_params <- create_alignment_params()

# Simulate the alignment
alignment <- sim_true_alignment(
   true_phylogeny = phylogeny,
   alignment_params = alignment_params,
 )
check_alignment(alignment)