scistreer (version 1.2.1)

perform_nni: Maximum likelihood tree search via NNI

Description

Maximum likelihood tree search via NNI

Usage

perform_nni(
  tree_init,
  P,
  max_iter = 100,
  eps = 0.01,
  ncores = 1,
  verbose = TRUE
)

Value

multiPhylo List of trees corresponding to the rearrangement steps

Arguments

tree_init

phylo Intial tree

P

matrix Genotype probability matrix

max_iter

integer Maximum number of iterations

eps

numeric Tolerance threshold in likelihood difference for stopping

ncores

integer Number of cores to use

verbose

logical Verbosity

Examples

tree_list = perform_nni(tree_upgma, P_small)