View source: R/create_equal_alignment_explicit.R
create_equal_alignment_explicit | R Documentation |
function create an alignment with identical information content, using the explicit method to simulate substitutions
create_equal_alignment_explicit(
input_tree,
sub_rate,
alignment_result,
verbose = FALSE
)
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 |
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.
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