CI                      Consistency Index and Retention Index
Laurasiatherian         Laurasiatherian data (AWCMEE)
NJ                      Neighbor-Joining
SH.test                 Shimodaira-Hasegawa Test
SOWH.test               Swofford-Olsen-Waddell-Hillis Test
add.tips                Add tips to a tree
allSplits               Splits representation of graphs and trees.
allTrees                Compute all trees topologies.
ancestral.pml           Ancestral character reconstruction.
as.networx              Conversion among phylogenetic network 0bjects
bab                     Branch and bound for finding all most
                        parsimonious trees
bootstrap.pml           Bootstrap
chloroplast             Chloroplast alignment
cladePar                Utility function to plot.phylo
coalSpeciesTree         Species Tree
codonTest               codonTest
consensusNet            Computes a consensusNetwork from a list of
                        trees Computes a 'networx' object from a
                        collection of splits.
cophenetic.networx      Pairwise Distances from a Phylogenetic Network
createLabel             Compare splits and add support values to an
                        object
delta.score             Computes the delta score
densiTree               Plots a densiTree.
designTree              Compute a design matrix or non-negative LS
discrete.gamma          Internal maximum likelihood functions.
dist.hamming            Pairwise Distances from Sequences
dist.p                  Pairwise Polymorphism P-Distances from DNA
                        Sequences
distanceHadamard        Distance Hadamard
fitch                   Parsimony tree.
getClans                Clans, slices and clips
getRoot                 Tree manipulation
hadamard                Hadamard Matrices and Fast Hadamard
                        Multiplication
identify.networx        Identify splits in a network
ldfactorial             Arithmetic Operators
lento                   Lento plot
mast                    Maximum agreement subtree
maxCladeCred            Maximum clade credibility tree
modelTest               ModelTest
multiphyDat2pmlPart     Partition model.
neighborNet             Computes a neighborNet from a distance matrix
nni                     Tree rearrangements.
phangorn-package        Phylogenetic analysis in R
phyDat                  Conversion among Sequence Formats
plot.networx            plot phylogenetic networks
pml.control             Likelihood of a tree.
pmlCluster              Stochastic Partitioning
pmlMix                  Phylogenetic mixture model
read.aa                 Read Amino Acid Sequences in a File
read.nexus.splits       Function to import and export splits and
                        networks
simSeq                  Simulate sequences.
splitsNetwork           Phylogenetic Network
superTree               Super Tree methods
treedist                Distances between trees
upgma                   UPGMA and WPGMA
writeDist               Writing and reading distances in phylip and
                        nexus format
yeast                   Yeast alignment (Rokas et al.)
