phangorn2.12.1 package

Draw Confidences Intervals on Phylogenies

Assign and compute edge lengths from a sample of trees

Add tips to a tree

Compare splits and add support values to an object

Compute all trees topologies.

tree utility function

Ancestral character reconstruction.

Conversion among phylogenetic network objects

Conversion among Sequence Formats

Splits representation of graphs and trees.

Branch and bound for finding all most parsimonious trees

Summaries of alignments

Bootstrap

Consistency Index and Retention Index

Utility function to plot.phylo

Species Tree

codonTest

Computes a consensusNetwork from a list of trees Computes a networxo...

Pairwise Distances from a Phylogenetic Network

Computes the $\delta$ score

Plots a densiTree.

Compute a design matrix or non-negative LS

Arithmetic Operators

Discrete Gamma and Beta distribution

Pairwise Distances from Sequences

Pairwise Polymorphism P-Distances from DNA Sequences

Distance Hadamard

Translate nucleic acid sequences into codons

Treat gaps as a state

Clans, slices and clips

Hadamard Matrices and Fast Hadamard Multiplication

Identify splits in a network

Plot of a Sequence Alignment

Replace leading and trailing alignment gaps with an ambiguous state

Lento plot

Maximum agreement subtree

Maximum clade credibility tree

Tree manipulation

ModelTest

Computes a neighborNet from a distance matrix

Neighbor-Joining

Tree rearrangements.

Parsimony tree.

Internal phangorn Functions

phangorn: Phylogenetic Reconstruction and Analysis

Generic functions for class phyDat

Plot ancestral character on a tree

plot phylogenetic networks

Plot phylogeny of a pml object

Plotting trees with bootstrap values

Likelihood of a tree.

Auxiliary for Controlling Fitting

Internal maximum likelihood functions.

Likelihood of a tree.

Stochastic Partitioning

Phylogenetic mixture model

Partition model.

Function to import partitioned data from nexus files

Function to import and export splits and networks

Import and export sequence alignments

Objects exported from other packages

Shimodaira-Hasegawa Test

Simulate sequences.

Swofford-Olsen-Waddell-Hillis Test

Phylogenetic Network

Super Tree methods

Transfer Bootstrap

Distances between trees

UPGMA, WPGMA and sUPGMA

Export and convenience functions for ancestral reconstructions

Export pml objects

Writing and reading distances in phylip and nexus format