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 |
ChangeBrlen | Change the branch length |
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 |
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 |
loglikeSP | loglikelihood of the species tree, i.e., Rannala and Yang... |
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 |
nancdist | Get ancestors and their divergence times |
NJst | calculate the NJst tree |
noclock2clock | Convert a non-clocklike tree to a clocklike tree |
node2name | Replace node numbers by species names in a tree string |
node.height | Calculate node height |
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 |
phybase2phylo | Convert between phybase's modified newick and ape phylo |
phybase-package | Basic functions for Phylogenetic trees |
plottree | Write a tree file |
popsize | Population size of the most recent common ancestor of two... |
populationMutation | Change branch lengths of a gene tree in the non-clocklike... |
postdist.tree | Calculate posterior probabilities of trees |
rank.nodes | Node ranks (internal use only) |
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 |
rooted.tree | An example of rooted trees |
rootoftree | Root of a tree |
root.tree | Root a tree |
sctree | Shallowest Coalescence Tree |
sim.coaltree | Simulate a coalescence tree |
sim.coaltree.phylo | Simulate a gene tree from species tree in ape's phylo format |
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 |
upgmaR | 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 |
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