# Phylogenetic Analysis in R

## Documentation for package ‘phangorn’ version 2.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K 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 | Compare splits and add support values to an object
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.AAbin.phyDat | Conversion among Sequence Formats
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.phyDat | Conversion among Sequence Formats
as.networx | Phylogenetic networks
as.networx.phylo | 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.phyDat.MultipleAlignment | 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.
cophenetic.networx | Pairwise Distances from a Phylogenetic Network
cophenetic.splits | Pairwise Distances from a Phylogenetic Network
countCycles | Splits representation of graphs and trees.
createLabel | Compare splits and add support values to an object

## -- D --

delta.score | Computes the delta score
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

## -- I --

image.phyDat | Conversion among Sequence Formats

## -- K --

KF.dist | Distances between trees

## -- L --

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

## -- M --

matchSplits | Splits representation of graphs and trees.
maxCladeCred | Maximum clade credibility tree
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.
path.dist | Distances between trees
phangorn | Phylogenetic analysis in R
phyDat | Conversion among Sequence Formats
phyDat2alignment | Conversion among Sequence Formats
phyDat2MultipleAlignment | 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 | Compare splits and add support values to an object
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.networx | Phylogenetic networks
read.nexus.splits | Splits representation of graphs and trees.
read.phyDat | Conversion among Sequence Formats
readDist | Pairwise Distances from Sequences
removeUndeterminedSites | Conversion among Sequence Formats
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 --

unique.phyDat | Conversion among Sequence Formats
UNJ | Neighbor-Joining
upgma | UPGMA and WPGMA

## -- W --

wpgma | UPGMA and WPGMA
wRF.dist | Distances between trees
write.nexus.networx | Phylogenetic networks
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.)