# Phylogenetic Reconstruction and Analysis

## Documentation for package ‘phangorn’ version 2.12.1

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

## Help Pages

A B C D E F G H I K L M N O P R S T U V 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
add_mutations | Plot ancestral character on a tree
add_support | Plotting trees with bootstrap values
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.
anc_pars | Ancestral character reconstruction.
anc_pml | Ancestral character reconstruction.
anova.pml | Likelihood of a tree.
as.AAbin.phyDat | Conversion among Sequence Formats
as.ancestral | Export and convenience functions for ancestral reconstructions
as.bitsplits.splits | Splits representation of graphs and trees.
as.character.phyDat | Conversion among Sequence Formats
as.data.frame.ancestral | Ancestral character reconstruction.
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.AAbin | Conversion among Sequence Formats
as.phyDat.AAStringSet | Conversion among Sequence Formats
as.phyDat.alignment | Conversion among Sequence Formats
as.phyDat.ancestral | Ancestral character reconstruction.
as.phyDat.character | Conversion among Sequence Formats
as.phyDat.data.frame | Conversion among Sequence Formats
as.phyDat.DNAbin | Conversion among Sequence Formats
as.phyDat.DNAStringSet | 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.
as.StringSet | Conversion among Sequence Formats
as.StringSet.phyDat | Conversion among Sequence Formats

## -- 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.
composition_test | Summaries of alignments
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
dna2aa | Translate nucleic acid sequences into codons
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 --

gap_as_ambiguous | Treat gaps as a state
gap_as_state | Treat gaps as a state
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
has_gap_state | Treat gaps as a state

## -- I --

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

## -- K --

keep_as_tip | Tree manipulation
KF.dist | Distances between trees

## -- L --

latag2n.phyDat | Replace leading and trailing alignment gaps with an ambiguous state
Laurasiatherian | Laurasiatherian data (AWCMEE)
ldfactorial | Arithmetic Operators
lento | Lento plot
lli | Internal maximum likelihood functions.
logLik.pml | Likelihood of a tree.

## -- 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
plot.pml | Plot phylogeny of a pml object
plotAnc | Plot ancestral character on a tree
plotBS | Plotting trees with bootstrap values
plotRates | Discrete Gamma and Beta distribution
plotSeqLogo | Plot ancestral character on a tree
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.ancestral | Export and convenience functions for ancestral reconstructions
print.phyDat | Generic functions for class phyDat
print.pml | Likelihood of a tree.
print.splits | Splits representation of graphs and trees.
pruneTree | Tree manipulation

## -- R --

random.addition | Parsimony tree.
ratchet.control | Auxiliary for Controlling Fitting
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.partitions | Function to import partitioned data from nexus files
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
supgma | UPGMA, WPGMA and sUPGMA

## -- 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, WPGMA and sUPGMA

## -- V --

vcov.pml | Likelihood of a tree.

## -- W --

wpgma | UPGMA, WPGMA and sUPGMA
wRF.dist | Distances between trees
write.ancestral | Export and convenience functions for ancestral reconstructions
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.pml | Export pml objects
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