create_equal_alignment_explicit: function create an alignment with identical information...

In thijsjanzen/nodeSub: Simulate DNA Alignments Using Node Substitutions

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.

thijsjanzen/nodeSub documentation built on Nov. 15, 2023, 2:44 p.m.