Man pages for phangorn
Phylogenetic Reconstruction and Analysis

addConfidencesCompare splits and add support values to an object
add.tipsAdd tips to a tree
allTreesCompute all trees topologies.
Ancestorstree utility function
ancestral.pmlAncestral character reconstruction.
as.networxPhylogenetic networks
as.splitsSplits representation of graphs and trees.
babBranch and bound for finding all most parsimonious trees
chloroplastChloroplast alignment
CIConsistency Index and Retention Index
cladeParUtility function to plot.phylo
coalSpeciesTreeSpecies Tree
consensusNetComputes a consensusNetwork from a list of trees Computes a...
cophenetic.networxPairwise Distances from a Phylogenetic Network
delta.scoreComputes the delta score
densiTreePlots a densiTree.
designTreeCompute a design matrix or non-negative LS
dfactorialArithmetic Operators
distanceHadamardDistance Hadamard
dist.hammingPairwise Distances from Sequences
dist.pPairwise Polymorphism P-Distances from DNA Sequences
getClansClans, slices and clips
hadamardHadamard Matrices and Fast Hadamard Multiplication
identify.networxIdentify splits in a network
LaurasiatherianLaurasiatherian data (AWCMEE)
lentoLento plot
mastMaximum agreement subtree
maxCladeCredMaximum clade credibility tree
midpointTree manipulation
neighborNetComputes a neighborNet from a distance matrix
nniTree rearrangements.
parsimonyParsimony tree.
phangorn-internalInternal phangorn Functions
phangorn-packagePhylogenetic analysis in R
phyDatConversion among Sequence Formats
pmlLikelihood of a tree.
pmlClusterStochastic Partitioning
pml.fitInternal maximum likelihood functions.
pmlMixPhylogenetic mixture model
pmlPartPartition model.
read.aaRead Amino Acid Sequences in a File to import and export splits and networks
SH.testShimodaira-Hasegawa Test
simSeqSimulate sequences.
SOWH.testSwofford-Olsen-Waddell-Hillis Test
splitsNetworkPhylogenetic Network
superTreeSuper Tree methods
treedistDistances between trees
upgmaUPGMA and WPGMA
writeDistWriting and reading distances in phylip and nexus format
yeastYeast alignment (Rokas et al.)
phangorn documentation built on Feb. 16, 2018, 1:02 a.m.