Package index • phangorn

All functions

CI() RI(): Consistency Index and Retention Index

Laurasiatherian: Laurasiatherian data (AWCMEE)

NJ() UNJ(): Neighbor-Joining

SH.test(): Shimodaira-Hasegawa Test

SOWH.test(): Swofford-Olsen-Waddell-Hillis Test

acctran() parsimony_edgelength(): Assign edge length to tree

add.tips(): Add tips to a tree

addConfidences() presenceAbsence() createLabel(): Compare splits and add support values to an object

add_ci() add_boxplot(): Draw Confidences Intervals on Phylogenies

add_edge_length(): Assign and compute edge lengths from a sample of trees

allTrees(): Compute all trees topologies.

ancestral.pml() anc_pml() ancestral.pars() anc_pars() pace(): Ancestral character reconstruction.

as.networx(): Conversion among phylogenetic network objects

phyDat() as.phyDat() phyDat2alignment() as.StringSet() as.MultipleAlignment(<phyDat>) as.character(<phyDat>) as.data.frame(<phyDat>) as.DNAbin(<phyDat>) as.AAbin(<phyDat>) genlight2phyDat() acgt2ry() unalign(): Conversion among Sequence Formats

allSplits() allCircularSplits() as.splits() as.matrix(<splits>) as.Matrix(<splits>) print(<splits>) c(<splits>) unique(<splits>) as.prop.part(<splits>) as.bitsplits(<splits>) compatible(): Splits representation of graphs and trees.

bab(): Branch and bound for finding all most parsimonious trees

baseFreq() glance(<phyDat>) composition_test() summary(<phyDat>) print(<summary.phyDat>): Summaries of alignments

bootstrap.pml() bootstrap.phyDat(): Bootstrap

chloroplast: Chloroplast alignment

cladePar(): Utility function to plot.phylo

coalSpeciesTree(): Species Tree

codonTest(): codonTest

consensusNet(): Computes a consensusNetwork from a list of trees Computes a networx object from a collection of splits.

cophenetic(<networx>): Pairwise Distances from a Phylogenetic Network

delta.score(): Computes the \(\delta\) score

densiTree(): Plots a densiTree.

designTree() nnls.tree() nnls.phylo() nnls.splits() nnls.networx() designSplits(): Compute a design matrix or non-negative LS

ldfactorial() dfactorial(): Arithmetic Operators

discrete.gamma() discrete.beta() plot_gamma_plus_inv() plotRates(): Discrete Gamma and Beta distribution

dist.hamming() dist.ml() dist.logDet(): Pairwise Distances from Sequences

dist.p(): Pairwise Polymorphism P-Distances from DNA Sequences

distanceHadamard(): Distance Hadamard

dna2codon() codon2dna() dna2aa(): Translate nucleic acid sequences into codons

gap_as_state() gap_as_ambiguous() has_gap_state(): Treat gaps as a state

getClans() getSlices() getClips() getDiversity() summary(<clanistics>) diversity(): Clans, slices and clips

hadamard() fhm() h4st() h2st(): Hadamard Matrices and Fast Hadamard Multiplication

identify(<networx>): Identify splits in a network

image(<phyDat>) image(<ancestral>): Plot of a Sequence Alignment

latag2n.phyDat(): Replace leading and trailing alignment gaps with an ambiguous state

lento(): Lento plot

mast(): Maximum agreement subtree

maxCladeCred() mcc() allCompat(): Maximum clade credibility tree

getRoot() midpoint() pruneTree() keep_as_tip(): Tree manipulation

mites: Morphological characters of Mites (Schäffer et al. 2010)

modelTest(): ModelTest

neighborNet(): Computes a neighborNet from a distance matrix

nni() rNNI() rSPR(): Tree rearrangements.

fitch() random.addition() parsimony() optim.parsimony() pratchet() sankoff(): Parsimony tree.

print(<phyDat>) cbind(<phyDat>) rbind(<phyDat>) c(<phyDat>) subset(<phyDat>) `[`(<phyDat>) unique(<phyDat>) removeUndeterminedSites() removeAmbiguousSites() allSitePattern(): Generic functions for class phyDat

plotAnc() plotSeqLogo() add_mutations(): Plot ancestral character on a tree

plot(<networx>): plot phylogenetic networks

plot(<pml>): Plot phylogeny of a pml object

plotBS() add_support(): Plotting trees with bootstrap values

as.pml() update(<pml>) pml() optim.pml() logLik(<pml>) anova(<pml>) vcov(<pml>) print(<pml>): Likelihood of a tree.

pml.control() ratchet.control(): Auxiliary for Controlling Fitting

lli() pml.fit(): Internal maximum likelihood functions.

pmlCluster(): Stochastic Partitioning

pmlMix(): Phylogenetic mixture model

multiphyDat2pmlPart() pmlPart2multiPhylo() pmlPart(): Partition model.

pml_bb(): Likelihood of a tree.

read.nexus.partitions(): Function to import partitioned data from nexus files

read.nexus.splits() write.nexus.splits() write.nexus.networx() read.nexus.networx() write.splits(): Function to import and export splits and networks

read.phyDat() write.phyDat(): Import and export sequence alignments

simSeq(): Simulate sequences.

splitsNetwork(): Phylogenetic Network

superTree(): Super Tree methods

terraces(): Explore likelihood parsimony surface

transferBootstrap(): Transfer Bootstrap

treedist() sprdist() SPR.dist() RF.dist() wRF.dist() KF.dist() path.dist(): Distances between trees

upgma() wpgma() supgma(): UPGMA, WPGMA and sUPGMA

write.ancestral() as.ancestral() print(<ancestral>) as.phyDat(<ancestral>) as.data.frame(<ancestral>): Export and convenience functions for ancestral reconstructions

write.pml(): Export pml objects

writeDist() write.nexus.dist() readDist() read.nexus.dist() unique(<dist>): Writing and reading distances in phylip and nexus format

yeast: Yeast alignment (Rokas et al.)