Optimize.TopologySearch: Optimize.TopologySearch: function to find the ML topology...

In radamsRHA/SpeciesTopoTestR: Likelihood-based tests of species topologies in R

Optimize.TopologySearch: function to find the ML topology using STELLS

Description

This function returns an optimized species topology and its maximized likelihood

Usage

Optimize.TopologySearch(handle.GeneTrees, string.PathDir)

Arguments

handle.GeneTrees	Phylo object containing a list of gene trees
string.PathDir	String defining the path to a parent directory used for optimizing species tree
numeric.Stells_algorthm	Numeric defining with algorithm of STELLS to use: 0 or 1

Value

handle.Optimized_SpeciesTree Species tree with branch lengths (in coalescent units) that has been optimized with STELLS

numeric.MaximizedLnL Numeric containing the maximum likelihood given the optimized branch lengths of the species tree

radamsRHA/SpeciesTopoTestR documentation built on Sept. 5, 2022, 7:37 p.m.