Man pages for phangorn
Phylogenetic Reconstruction and Analysis

add_ciDraw Confidences Intervals on Phylogenies
addConfidencesCompare splits and add support values to an object
add_edge_lengthAssign and compute edge lengths from a sample of trees
add.tipsAdd tips to a tree
allTreesCompute all trees topologies.
Ancestorstree utility function
ancestral.pmlAncestral character reconstruction.
as.networxConversion among phylogenetic network objects
as.phyDatConversion among Sequence Formats
as.splitsSplits representation of graphs and trees.
babBranch and bound for finding all most parsimonious trees
baseFreqSummaries of alignments
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
discrete.gammaDiscrete Gamma and Beta distribution
distanceHadamardDistance Hadamard
dist.hammingPairwise Distances from Sequences
dist.pPairwise Polymorphism P-Distances from DNA Sequences
dna2codonTranslate nucleic acid sequences into codons
getClansClans, slices and clips
hadamardHadamard Matrices and Fast Hadamard Multiplication
identify.networxIdentify splits in a network
image.phyDatPlot of a Sequence Alignment
LaurasiatherianLaurasiatherian data (AWCMEE)
lentoLento plot
mastMaximum agreement subtree
maxCladeCredMaximum clade credibility tree
midpointTree manipulation
mitesMorphological characters of Mites (Schäffer et al. 2010)
neighborNetComputes a neighborNet from a distance matrix
nniTree rearrangements.
parsimonyParsimony tree.
phangorn-internalInternal phangorn Functions
phangorn-packagephangorn: Phylogenetic Reconstruction and Analysis
phyDatGeneric functions for class phyDat
plotBSPlotting trees with bootstrap values
plot.networxplot phylogenetic networks
pmlLikelihood of a tree.
pml_bbLikelihood of a tree.
pmlClusterStochastic Partitioning
pml.controlAuxiliary for Controlling Fitting
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
read.phyDatImport and export sequence alignments
reexportsObjects exported from other packages
SH.testShimodaira-Hasegawa Test
simSeqSimulate sequences.
SOWH.testSwofford-Olsen-Waddell-Hillis Test
splitsNetworkPhylogenetic Network
superTreeSuper Tree methods
transferBootstrapTransfer Bootstrap
treedistDistances between trees
upgmaUPGMA and WPGMA
writeDistWriting and reading distances in phylip and nexus format
yeastYeast alignment (Rokas et al.)
phangorn documentation built on Jan. 23, 2023, 5:37 p.m.