Phylogenetic Reconstruction and Analysis

Documentation for package ‘phangorn’ version 2.11.1

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A B C D E F G H I K L M N O P R S T U W Y misc

-- A --

acctran	Parsimony tree.
acgt2ry	Conversion among Sequence Formats
add.tips	Add tips to a tree
addConfidences	Compare splits and add support values to an object
addConfidences.phylo	Compare splits and add support values to an object
addTrivialSplits	Splits representation of graphs and trees.
add_boxplot	Draw Confidences Intervals on Phylogenies
add_ci	Draw Confidences Intervals on Phylogenies
add_edge_length	Assign and compute edge lengths from a sample of trees
AICc	ModelTest
allCircularSplits	Splits representation of graphs and trees.
allCompat	Maximum clade credibility tree
allSitePattern	Generic functions for class phyDat
allSplits	Splits representation of graphs and trees.
allTrees	Compute all trees topologies.
ancestral.pars	Ancestral character reconstruction.
ancestral.pml	Ancestral character reconstruction.
as.AAbin.phyDat	Conversion among Sequence Formats
as.bitsplits.splits	Splits representation of graphs and trees.
as.character.phyDat	Conversion among Sequence Formats
as.data.frame.phyDat	Conversion among Sequence Formats
as.DNAbin.phyDat	Conversion among Sequence Formats
as.Matrix	Splits representation of graphs and trees.
as.Matrix.splits	Splits representation of graphs and trees.
as.matrix.splits	Splits representation of graphs and trees.
as.MultipleAlignment	Conversion among Sequence Formats
as.MultipleAlignment.phyDat	Conversion among Sequence Formats
as.networx	Conversion among phylogenetic network objects
as.networx.phylo	Conversion among phylogenetic network objects
as.networx.splits	Conversion among phylogenetic network objects
as.phyDat	Conversion among Sequence Formats
as.phyDat.alignment	Conversion among Sequence Formats
as.phyDat.character	Conversion among Sequence Formats
as.phyDat.data.frame	Conversion among Sequence Formats
as.phyDat.DNAbin	Conversion among Sequence Formats
as.phyDat.factor	Conversion among Sequence Formats
as.phyDat.matrix	Conversion among Sequence Formats
as.phyDat.MultipleAlignment	Conversion among Sequence Formats
as.phylo.splits	Splits representation of graphs and trees.
as.pml	Likelihood of a tree.
as.prop.part.splits	Splits representation of graphs and trees.
as.splits	Splits representation of graphs and trees.
as.splits.bitsplits	Splits representation of graphs and trees.
as.splits.multiPhylo	Splits representation of graphs and trees.
as.splits.networx	Splits representation of graphs and trees.
as.splits.phylo	Splits representation of graphs and trees.

-- B --

bab	Branch and bound for finding all most parsimonious trees
baseFreq	Summaries of alignments
bootstrap.phyDat	Bootstrap
bootstrap.pml	Bootstrap
BranchAndBound	Branch and bound for finding all most parsimonious trees

-- C --

c.phyDat	Generic functions for class phyDat
c.splits	Splits representation of graphs and trees.
cbind.phyDat	Generic functions for class phyDat
chloroplast	Chloroplast alignment
CI	Consistency Index and Retention Index
cladePar	Utility function to plot.phylo
coalSpeciesTree	Species Tree
codon2dna	Translate nucleic acid sequences into codons
codonTest	codonTest
compatible	Splits representation of graphs and trees.
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
cophenetic.splits	Pairwise Distances from a Phylogenetic Network
createLabel	Compare splits and add support values to an object

-- D --

delta.score	Computes the delta score
densiTree	Plots a densiTree.
designSplits	Compute a design matrix or non-negative LS
designTree	Compute a design matrix or non-negative LS
dfactorial	Arithmetic Operators
discrete.beta	Discrete Gamma and Beta distribution
discrete.gamma	Discrete Gamma and Beta distribution
dist.hamming	Pairwise Distances from Sequences
dist.logDet	Pairwise Distances from Sequences
dist.ml	Pairwise Distances from Sequences
dist.p	Pairwise Polymorphism P-Distances from DNA Sequences
distanceHadamard	Distance Hadamard
distinct.splits	Splits representation of graphs and trees.
diversity	Clans, slices and clips
dna2codon	Translate nucleic acid sequences into codons

-- E --

edQt	Internal maximum likelihood functions.

-- F --

fhm	Hadamard Matrices and Fast Hadamard Multiplication
fitch	Parsimony tree.

-- G --

genlight2phyDat	Conversion among Sequence Formats
getClans	Clans, slices and clips
getClips	Clans, slices and clips
getDiversity	Clans, slices and clips
getRoot	Tree manipulation
getSlices	Clans, slices and clips
glance.phyDat	Summaries of alignments

-- H --

h2st	Hadamard Matrices and Fast Hadamard Multiplication
h4st	Hadamard Matrices and Fast Hadamard Multiplication
hadamard	Hadamard Matrices and Fast Hadamard Multiplication

-- I --

identify.networx	Identify splits in a network
image.phyDat	Plot of a Sequence Alignment

-- K --

KF.dist

Distances between trees

-- L --

Laurasiatherian	Laurasiatherian data (AWCMEE)
ldfactorial	Arithmetic Operators
lento	Lento plot
lli	Internal maximum likelihood functions.

-- M --

mast	Maximum agreement subtree
matchSplits	Splits representation of graphs and trees.
maxCladeCred	Maximum clade credibility tree
mcc	Maximum clade credibility tree
midpoint	Tree manipulation
midpoint.multiPhylo	Tree manipulation
midpoint.phylo	Tree manipulation
mites	Morphological characters of Mites (Schäffer et al. 2010)
modelTest	ModelTest
multiphyDat2pmlPart	Partition model.

-- N --

neighborNet	Computes a neighborNet from a distance matrix
networx	Conversion among phylogenetic network objects
NJ	Neighbor-Joining
nni	Tree rearrangements.
nnls.networx	Compute a design matrix or non-negative LS
nnls.phylo	Compute a design matrix or non-negative LS
nnls.splits	Compute a design matrix or non-negative LS
nnls.tree	Compute a design matrix or non-negative LS

-- O --

optim.parsimony	Parsimony tree.
optim.pml	Likelihood of a tree.

-- P --

pace	Ancestral character reconstruction.
parsimony	Parsimony tree.
path.dist	Distances between trees
phyDat	Conversion among Sequence Formats
phyDat2alignment	Conversion among Sequence Formats
phyDat2MultipleAlignment	Conversion among Sequence Formats
plot.networx	plot phylogenetic networks
plotAnc	Ancestral character reconstruction.
plotBS	Plotting trees with bootstrap values
plotRates	Discrete Gamma and Beta distribution
plot_gamma_plus_inv	Discrete Gamma and Beta distribution
pml	Likelihood of a tree.
pml.control	Auxiliary for Controlling Fitting
pml.fit	Internal maximum likelihood functions.
pml.free	Internal maximum likelihood functions.
pml.init	Internal maximum likelihood functions.
pmlCluster	Stochastic Partitioning
pmlMix	Phylogenetic mixture model
pmlPart	Partition model.
pmlPart2multiPhylo	Partition model.
pml_bb	Likelihood of a tree.
pratchet	Parsimony tree.
presenceAbsence	Compare splits and add support values to an object
print.phyDat	Generic functions for class phyDat
print.splits	Splits representation of graphs and trees.
pruneTree	Tree manipulation

-- R --

random.addition	Parsimony tree.
ratchet.control	Auxiliary for Controlling Fitting
read.aa	Read Amino Acid Sequences in a File
read.nexus.dist	Writing and reading distances in phylip and nexus format
read.nexus.networx	Function to import and export splits and networks
read.nexus.splits	Function to import and export splits and networks
read.phyDat	Import and export sequence alignments
readDist	Writing and reading distances in phylip and nexus format
removeAmbiguousSites	Generic functions for class phyDat
removeTrivialSplits	Splits representation of graphs and trees.
removeUndeterminedSites	Generic functions for class phyDat
RF.dist	Distances between trees
RI	Consistency Index and Retention Index
rNNI	Tree rearrangements.
rSPR	Tree rearrangements.

-- S --

sankoff	Parsimony tree.
SH.test	Shimodaira-Hasegawa Test
simSeq	Simulate sequences.
simSeq.phylo	Simulate sequences.
simSeq.pml	Simulate sequences.
SOWH.test	Swofford-Olsen-Waddell-Hillis Test
splits	Splits representation of graphs and trees.
splitsNetwork	Phylogenetic Network
SPR.dist	Distances between trees
sprdist	Distances between trees
subset.phyDat	Generic functions for class phyDat
summary.clanistics	Clans, slices and clips
superTree	Super Tree methods

-- T --

transferBootstrap	Transfer Bootstrap
treedist	Distances between trees

-- U --

unique.dist	Writing and reading distances in phylip and nexus format
unique.phyDat	Generic functions for class phyDat
unique.splits	Splits representation of graphs and trees.
UNJ	Neighbor-Joining
upgma	UPGMA and WPGMA

-- W --

wpgma	UPGMA and WPGMA
wRF.dist	Distances between trees
write.nexus.dist	Writing and reading distances in phylip and nexus format
write.nexus.networx	Function to import and export splits and networks
write.nexus.splits	Function to import and export splits and networks
write.phyDat	Import and export sequence alignments
write.splits	Function to import and export splits and networks
writeDist	Writing and reading distances in phylip and nexus format

-- Y --

yeast

Yeast alignment (Rokas et al.)

-- misc --

[.phyDat

Generic functions for class phyDat