ChangeBrlen             Change the branch length
FindSpnodeDownGenenode
                        Internal function
PhyBase                 Basic functions for Phylogenetic trees
ancandtime              Get ancestors and their divergence times
ancestor                Find the ancestral nodes of a node
bootstrap               Bootstrap sequences
bootstrap.mulgene       Bootstrap sequences from multiple loci
change.root             Change tree root
coal.sptree             Estimating species trees using average
                        coalescence times
coaltime                Coalescence time of two nodes
consense                Consensus tree
del.node                Delete a node from the tree
genetree.vector         Construct gene tree vectors from multiple loci
getcoaltime             Get coalescence times
getncoal                internal function
is.clock                Is a clock tree or not
is.rootedtree           Is the tree rooted or not
maxtree                 Maximum Tree
mrca.2nodes             Find the most recent common ancestor of two
                        nodes
mrca.nodes              Find the most recent common ancestor of
                        multiple nodes
mutation_exp            Generate mutation rates for populations in the
                        species tree
name2node               Replace species names by their node numbers
noclock2clock           Convert a non-clocklike tree to a clocklike
                        tree
node.height             Calculate node height
node2name               Replace node numbers by species names in a tree
                        string
offspring.nodes         Find the offspring nodes
offspring.nodes.string
                        Find offspring nodes (internal use only)
offspring.species       Find the species nodes
pair.dist               Calculate all pairwise distances among taxa in
                        the tree
pair.dist.dna           Calculate pairwise distances among DNA
                        sequences
pair.dist.mulseq        Calculate pairwise distances among species
partition.tree          partition a tree
plottree                Write a tree file
popsize                 Population size of the most recent common
                        ancestor of two nodes
populationMutation      Change branch lengths of a gene tree in the
                        non-clocklike species tree model (internal use
                        only)
postdist.tree           Calculate posterior probabilities of trees
rank.nodes              Node ranks (internal use only)
rannalandyang           Rannala and Yang's formula
rdirichlet              Generate random numbers from the dirichlet
                        distribution
read.dna.seq            Read sequences from files
read.tree.nodes         Read tree nodes
read.tree.string        Read tree strings from a tree file
root.tree               Root a tree
rooted.tree             An example of rooted trees
rootoftree              Root of a tree
sctree                  Shallowest Coalescence Tree
sim.coaltree            Simulate a coalescence tree
sim.coaltree.sp         simulate a gene tree from the species tree
sim.coaltree.sp.mu      Simulate a gene tree from the non-clock species
                        tree model
sim.dna                 Simulate DNA sequences from substitution models
simSeqfromSp            simulate DNA sequences from a species tree
simnucleotide           Intrinsic function used in sim.dna
site.pattern            Site patterns
sortmat                 Sort a matrix
species.name            Species names in a tree string
spstructure             Create a sequence-species relationship
sptree                  A species tree
star.sptree             Build a STAR tree
steac.sptree            Build a STEAC tree
subtree                 Subtree
subtree.length          Calculate total branch length of a tree
swap.nodes              Swap two nodes
treedist                Distance between two trees
tripleProb              Probability of a set of rooted triples
tripleloglike           Loglikehood of Triples
triplenumber            Internal function
triplepara              Internal function
unrooted.tree           An example of unrooted trees
unroottree              Unroot a tree
upgma                   UPGMA tree
write.dna               Write sequences to a Nexus file
write.subtree           Write a sub-tree into a string
write.tree.string       Write a tree file
