Ancestors               tree utility function
Laurasiatherian         Laurasiatherian data (AWCMEE)
NJ                      Neighbor-Joining
SH.test                 Shimodaira-Hasegawa Test
allTrees                Compute all trees topologies.
bootstrap.pml           Bootstrap
chloroplast             Chloroplast alignment
designTree              Compute a design matrix
dfactorial              Arithmetic Operators
dist.hamming            Pairwise Distances from Sequences
distanceHadamard        Distance Hadamard
hadamard                Hadamard Matrices and Fast Hadamard
                        Multiplication
nni                     Tree rearrangements.
parsimony               Parsimony tree.
phyDat                  Conversion among Sequence Formats
pml                     Likelihood of a tree.
pmlCluster              Stochastic Partitioning
pmlMix                  Phylogenetic mixture model
pmlPart                 Partition model.
read.aa                 Read Amino Acid Sequences in a File
simSeq                  Simulate sequences.
splitsNetwork           Phylogenetic Network
treedist                Distances between trees
upgma                   UPGMA
yeast                   Yeast alignment (Rokas et al.)
