phangorn

tree utility function

Consistency Index and Retention Index

Laurasiatherian data (AWCMEE)

Neighbor-Joining

Shimodaira-Hasegawa Test

Swofford-Olsen-Waddell-Hillis Test

Add tips to a tree

Compare splits and add support values to an object

Compute all trees topologies.

Ancestral character reconstruction.

Conversion among phylogenetic network objects

Splits representation of graphs and trees.

Branch and bound for finding all most parsimonious trees

Bootstrap

Chloroplast alignment

Utility function to plot.phylo

Species Tree

codonTest

Computes a consensusNetwork from a list of trees Computes a networx object from a collection of splits.

Pairwise Distances from a Phylogenetic Network

Computes the δ score

Plots a densiTree.

Compute a design matrix or non-negative LS

Arithmetic Operators

Discrete Gamma function

Pairwise Distances from Sequences

Pairwise Polymorphism P-Distances from DNA Sequences

Distance Hadamard

Translate nucleic acid sequences into codons

Clans, slices and clips

Hadamard Matrices and Fast Hadamard Multiplication

Identify splits in a network

Lento plot

Maximum agreement subtree

Maximum clade credibility tree

Tree manipulation

ModelTest

Computes a neighborNet from a distance matrix

Tree rearrangements.

Parsimony tree.

Internal phangorn Functions

Phylogenetic analysis in R

Conversion among Sequence Formats

plot phylogenetic networks

Plotting trees with bootstrap values

Likelihood of a tree.

Internal maximum likelihood functions.

Stochastic Partitioning

Phylogenetic mixture model

Partition model.

Read Amino Acid Sequences in a File

Function to import and export splits and networks

Import and export sequence alignments

Objects exported from other packages

Simulate sequences.

Phylogenetic Network

Super Tree methods

Distances between trees

UPGMA and WPGMA

Writing and reading distances in phylip and nexus format

Yeast alignment (Rokas et al.)