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
acctran                 Parsimony tree.
add.tips                Add tips to a tree
addConfidences          Compare splits and add support values to an
                        object
add_ci                  Draw Confidences Intervals on Phylogenies
add_edge_length         Assign and compute edge lengths from a sample
                        of trees
allSplits               Splits representation of graphs and trees.
allTrees                Compute all trees topologies.
ancestral.pml           Ancestral character reconstruction.
as.networx              Conversion among phylogenetic network objects
as.pml                  Likelihood of a tree.
bab                     Branch and bound for finding all most
                        parsimonious trees
baseFreq                Summaries of alignments
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
delta.score             Computes the delta score
densiTree               Plots a densiTree.
designTree              Compute a design matrix or non-negative LS
discrete.gamma          Discrete Gamma and Beta distribution
dist.hamming            Pairwise Distances from Sequences
dist.p                  Pairwise Polymorphism P-Distances from DNA
                        Sequences
distanceHadamard        Distance Hadamard
dna2codon               Translate nucleic acid sequences into codons
gap_as_state            Treat gaps as a state
getClans                Clans, slices and clips
getRoot                 Tree manipulation
hadamard                Hadamard Matrices and Fast Hadamard
                        Multiplication
identify.networx        Identify splits in a network
image.phyDat            Plot of a Sequence Alignment
latag2n.phyDat          Replace leading and trailing alignment gaps
                        with an ambiguous state
ldfactorial             Arithmetic Operators
lento                   Lento plot
lli                     Internal maximum likelihood functions.
mast                    Maximum agreement subtree
maxCladeCred            Maximum clade credibility tree
mites                   Morphological characters of Mites (Schäffer et
                        al. 2010)
modelTest               ModelTest
multiphyDat2pmlPart     Partition model.
neighborNet             Computes a neighborNet from a distance matrix
nni                     Tree rearrangements.
phyDat                  Conversion among Sequence Formats
plot.networx            plot phylogenetic networks
plot.pml                Plot phylogeny of a pml object
plotAnc                 Plot ancestral character on a tree
plotBS                  Plotting trees with bootstrap values
pml.control             Auxiliary for Controlling Fitting
pmlCluster              Stochastic Partitioning
pmlMix                  Phylogenetic mixture model
pml_bb                  Likelihood of a tree.
print.phyDat            Generic functions for class phyDat
read.nexus.partitions   Function to import partitioned data from nexus
                        files
read.nexus.splits       Function to import and export splits and
                        networks
read.phyDat             Import and export sequence alignments
simSeq                  Simulate sequences.
splitsNetwork           Phylogenetic Network
superTree               Super Tree methods
transferBootstrap       Transfer Bootstrap
treedist                Distances between trees
upgma                   UPGMA, WPGMA and sUPGMA
write.ancestral         Export and convenience functions for ancestral
                        reconstructions
write.pml               Export pml objects
writeDist               Writing and reading distances in phylip and
                        nexus format
yeast                   Yeast alignment (Rokas et al.)
