maximum_parsimony: Tree reconstruction via maximum parsimony

In Hoffmann-Lab/PhyloEpiGenomics: What the Package Does (One Line, Title Case)

Tree reconstruction via maximum parsimony

Description

maximum_parsimony determines the single, best fitting among the given tree topologies by maximum parsimony for given data. The respective determined costs wil be attached to the returning phylo object.

all_parsimony performs parsimony for all tree topologies given. The respective determined costs wil be attached to the phylo objects.

small_parsimony performs parsimony for one tree topology. The respective determined costs wil be attached to the phylo object.

Usage

maximum_parsimony(states_table, rooted_trees)

all_parsimony(states_table, rooted_trees)

small_parsimony(states_table, rooted_tree)

Arguments

states_table	Matrix or data frame containing numericals representing an alignment of interval or ordinal scaled states with sites as rows and species/strains as columns.
rooted_trees	List of rooted tree topologies of class phylo (library ape) to be analyzed.
rooted_tree	Rooted tree topology of class phylo (library ape) to be analyzed.

Details

These functions work on any interval scaled data such as methylation fractions or ordinal scaled data such as descritized methylation data. They do not work, however, on nominal scaled data, such as nucleotides.

Examples

test

Hoffmann-Lab/PhyloEpiGenomics documentation built on Feb. 12, 2023, 9:06 p.m.