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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
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() as.phyDat(<ancestral>) as.data.frame(<ancestral>) ancestral.pars() pace()
Ancestral character reconstruction.
as.networx()
Conversion among phylogenetic network objects
phyDat() as.phyDat() phyDat2alignment() as.MultipleAlignment(<phyDat>) as.character(<phyDat>) as.data.frame(<phyDat>) as.DNAbin(<phyDat>) as.AAbin(<phyDat>) genlight2phyDat() acgt2ry()
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()
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()
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>)
Plot of a Sequence Alignment
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.
acctran() fitch() random.addition() parsimony() optim.parsimony() pratchet() sankoff()
Parsimony tree.
print(<phyDat>) subset(<phyDat>) `[`(<phyDat>) unique(<phyDat>) removeUndeterminedSites() removeAmbiguousSites() allSitePattern()
Generic functions for class phyDat
plot(<networx>)
plot phylogenetic networks
plot(<pml>)
Plot phylogeny of a pml object
plotAnc()
Plot ancestral character on a tree
plotBS() add_support()
Plotting trees with bootstrap values
as.pml() pml() optim.pml() vcov(<pml>)
Likelihood of a tree.
pml.control() ratchet.control()
Auxiliary for Controlling Fitting
lli() edQt() pml.free() pml.init() 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.aa()
Read Amino Acid Sequences in a File
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
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
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.)