perform_nni: Maximum likelihood tree search via NNI

In scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale

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
)

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

Value

multiPhylo List of trees corresponding to the rearrangement steps

Examples

tree_list = perform_nni(tree_upgma, P_small)

scistreer documentation built on July 9, 2023, 5:54 p.m.