create_equal_alignment {nodeSub}

function create an alignment with identical information content

Description

function create an alignment with identical information content

Usage

create_equal_alignment(
  input_tree,
  sub_rate,
  alignment_result,
  sim_function = NULL,
  verbose = FALSE,
  node_time = NULL,
  input_alignment_type = "nodesub"
)

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

sim_function

function that accepts a tree, sequence length, rootsequence and substitution rate (in that order). Default is sim_normal

verbose

provide intermediate output

node_time

node time

input_alignment_type

was the input alignment simulated with a node substitution model or a normal substitution model? Used to calculate the twin mutation rate. Options are "nodesub" and "normal".

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.