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| 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 |
| ChangeBrlen | Change the branch length |
| 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 |
| FindSpnodeDownGenenode | Internal function |
| 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 |
| PhyBase | Basic functions for Phylogenetic trees |
| 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 |
| simnucleotide | Intrinsic function used in sim.dna |
| simSeqfromSp | simulate DNA sequences from a species tree |
| 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 |
| tripleloglike | Loglikehood of Triples |
| triplenumber | Internal function |
| triplepara | Internal function |
| tripleProb | Probability of a set of rooted triples |
| 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 |