Phylogenetic Analysis in R

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Documentation for package ‘phangorn’ version 1.99.14

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

phangorn-package Phylogenetic analysis in R

-- A --

acctran Parsimony tree.
acgt2ry Conversion among Sequence Formats
addConfidences Splits representation of graphs and trees.
addTrivialSplits Splits representation of graphs and trees.
AICc ModelTest
allSitePattern Conversion among Sequence Formats
allSplits Splits representation of graphs and trees.
allTrees Compute all trees topologies.
Ancestors tree utility function
ancestral.pars Ancestral character reconstruction.
ancestral.pml Ancestral character reconstruction.
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.networx Phylogenetic networks
as.networx.splits Phylogenetic networks
as.phyDat Conversion among Sequence Formats
as.phyDat.alignment Conversion among Sequence Formats
as.phyDat.DNAbin Conversion among Sequence Formats
as.phylo.splits Splits representation of graphs and trees.
as.prop.part.splits Splits representation of graphs and trees.
as.splits 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 Conversion among Sequence Formats
bootstrap.phyDat Bootstrap
bootstrap.pml Bootstrap
BranchAndBound Branch and bound for finding all most parsimonious trees

-- C --

c.phyDat Conversion among Sequence Formats
cbind.phyDat Conversion among Sequence Formats
Children tree utility function
chloroplast Chloroplast alignment
CI Parsimony tree.
cladePar Utility function to plot.phylo
coalSpeciesTree Super Tree and Species Tree methods
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.
countCycles Splits representation of graphs and trees.

-- D --

densiTree Plots a densiTree.
Descendants tree utility function
designSplits Compute a design matrix or non-negative LS
designTree Compute a design matrix or non-negative LS
dfactorial Arithmetic Operators
discrete.gamma Internal maximum likelihood functions.
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
diversity Clans, slices and clips

-- E --

edQt Internal maximum likelihood functions.

-- F --

fhm Hadamard Matrices and Fast Hadamard Multiplication
fitch Parsimony tree.

-- G --

getClans Clans, slices and clips
getClips Clans, slices and clips
getDiversity Clans, slices and clips
getRoot Tree manipulation
getSlices Clans, slices and clips

-- H --

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

-- L --

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

-- M --

midpoint Tree manipulation
modelTest ModelTest
mrca.phylo tree utility function

-- N --

neighborNet Computes a neighborNet from a distance matrix
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.
phangorn Phylogenetic analysis in R
phyDat Conversion among Sequence Formats
phyDat2alignment Conversion among Sequence Formats
plot.networx Phylogenetic networks
plotAnc Ancestral character reconstruction.
plotBS Bootstrap
pml Likelihood of a tree.
pml.control Likelihood of a tree.
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.
pmlPen Phylogenetic mixture model
PNJ Parsimony tree.
pratchet Parsimony tree.
presenceAbsence Splits representation of graphs and trees.
print.splits Splits representation of graphs and trees.
pruneTree Tree manipulation

-- R --

random.addition Parsimony tree.
read.aa Read Amino Acid Sequences in a File
read.nexus.splits Splits representation of graphs and trees.
read.phyDat Conversion among Sequence Formats
readDist Pairwise Distances from Sequences
RF.dist Distances between trees
RI Parsimony tree.
rNNI Tree rearrangements.
rSPR Tree rearrangements.

-- S --

sankoff Parsimony tree.
SH.test Shimodaira-Hasegawa Test
Siblings tree utility function
simSeq Simulate sequences.
simSeq.phylo Simulate sequences.
simSeq.pml Simulate sequences.
SOWH.test Swofford-Olsen-Waddell-Hillis Test
splitsNetwork Phylogenetic Network
subset.phyDat Conversion among Sequence Formats
superTree Super Tree and Species Tree methods

-- T --

treedist Distances between trees

-- U --

UNJ Neighbor-Joining
upgma UPGMA and WPGMA

-- W --

wpgma UPGMA and WPGMA
write.nexus.splits Splits representation of graphs and trees.
write.phyDat Conversion among Sequence Formats
write.splits Splits representation of graphs and trees.
writeDist Pairwise Distances from Sequences

-- Y --

yeast Yeast alignment (Rokas et al.)