Man pages for bomeara/phybase
Basic functions for phylogenetic analysis

ancandtimeGet ancestors and their divergence times
ancestorFind the ancestral nodes of a node
bootstrapBootstrap sequences
bootstrap.mulgeneBootstrap sequences from multiple loci
ChangeBrlenChange the branch length
change.rootChange tree root
coal.sptreeEstimating species trees using average coalescence times
coaltimeCoalescence time of two nodes
consenseConsensus tree
del.nodeDelete a node from the tree
FindSpnodeDownGenenodeInternal function
genetree.vectorConstruct gene tree vectors from multiple loci
getcoaltimeGet coalescence times
getncoalinternal function
is.clockIs a clock tree or not
is.rootedtreeIs the tree rooted or not
loglikeSPloglikelihood of the species tree, i.e., Rannala and Yang...
maxtreeMaximum Tree
mrca.2nodesFind the most recent common ancestor of two nodes
mrca.nodesFind the most recent common ancestor of multiple nodes
mutation_expGenerate mutation rates for populations in the species tree
name2nodeReplace species names by their node numbers
nancdistGet ancestors and their divergence times
NJstcalculate the NJst tree
noclock2clockConvert a non-clocklike tree to a clocklike tree
node2nameReplace node numbers by species names in a tree string
node.heightCalculate node height
offspring.nodesFind the offspring nodes
offspring.nodes.stringFind offspring nodes (internal use only)
offspring.speciesFind the species nodes
pair.distCalculate all pairwise distances among taxa in the tree
pair.dist.dnaCalculate pairwise distances among DNA sequences
pair.dist.mulseqCalculate pairwise distances among species
partition.treepartition a tree
phybase2phyloConvert between phybase's modified newick and ape phylo
phybase-packageBasic functions for Phylogenetic trees
plottreeWrite a tree file
popsizePopulation size of the most recent common ancestor of two...
populationMutationChange branch lengths of a gene tree in the non-clocklike...
postdist.treeCalculate posterior probabilities of trees
rank.nodesNode ranks (internal use only)
rdirichletGenerate random numbers from the dirichlet distribution
read.dna.seqRead sequences from files
read.tree.nodesRead tree nodes
read.tree.stringRead tree strings from a tree file
rooted.treeAn example of rooted trees
rootoftreeRoot of a tree
root.treeRoot a tree
sctreeShallowest Coalescence Tree
sim.coaltreeSimulate a coalescence tree
sim.coaltree.phyloSimulate a gene tree from species tree in ape's phylo format
sim.coaltree.spsimulate a gene tree from the species tree
sim.coaltree.sp.muSimulate a gene tree from the non-clock species tree model
sim.dnaSimulate DNA sequences from substitution models
simnucleotideIntrinsic function used in sim.dna
simSeqfromSpsimulate DNA sequences from a species tree
site.patternSite patterns
sortmatSort a matrix
species.nameSpecies names in a tree string
spstructureCreate a sequence-species relationship
sptreeA species tree
star.sptreeBuild a STAR tree
steac.sptreeBuild a STEAC tree
subtree.lengthCalculate total branch length of a tree
swap.nodesSwap two nodes
treedistDistance between two trees
tripleloglikeLoglikehood of Triples
triplenumberInternal function
tripleparaInternal function
tripleProbProbability of a set of rooted triples
unrooted.treeAn example of unrooted trees
unroottreeUnroot a tree
upgmaUPGMA tree
upgmaRUPGMA tree
write.dnaWrite sequences to a Nexus file
write.subtreeWrite a sub-tree into a string
write.tree.stringWrite a tree file
bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.