create_equal_alignment_explicit {nodeSub}

function create an alignment with identical information content, using the explicit method to simulate substitutions

Description

function create an alignment with identical information content, using the explicit method to simulate substitutions

Usage

create_equal_alignment_explicit(
  input_tree,
  sub_rate,
  alignment_result,
  verbose = FALSE
)

Arguments

input_tree

phylogeny for which to generate alignment

sub_rate

substitution rate used in the original phylogeny

alignment_result

result of sim_normal, sim_linked or sim_unlinked

verbose

provide intermediate output

Value

list with four properties: 1) alignment: the alignment itself, 2) adjusted rate: the substitution rate used to obtain identical information content 3) total_accumulated_substitutions: the total number of substitutions accumulated. 4) total_node_substitutions: total number of substitutions accumulated on the nodes 5) total_branch_substitutions: total number of substitutions accumulated on the branches.