phangorn: Phylogenetic Analysis in R

Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.

Install the latest version of this package by entering the following in R:
install.packages("phangorn")
AuthorKlaus Schliep [aut, cre], Emmanuel Paradis [aut], Leonardo de Oliveira Martins [aut], Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb]
Date of publication2017-04-03 20:40:30 UTC
MaintainerKlaus Schliep <klaus.schliep@gmail.com>
LicenseGPL (>= 2)
Version2.2.0
https://github.com/KlausVigo/phangorn

View on CRAN

Man pages

addConfidences: Compare splits and add support values to an object

allTrees: Compute all trees topologies.

Ancestors: tree utility function

ancestral.pml: Ancestral character reconstruction.

as.networx: Phylogenetic networks

as.splits: Splits representation of graphs and trees.

bab: Branch and bound for finding all most parsimonious trees

bootstrap.pml: Bootstrap

chloroplast: Chloroplast alignment

CI: Consistency Index and Retention Index

cladePar: Utility function to plot.phylo

coalSpeciesTree: Species Tree

consensusNet: Computes a consensusNetwork from a list of trees Computes a...

cophenetic.networx: Pairwise Distances from a Phylogenetic Network

delta.score: Computes the delta score

densiTree: Plots a densiTree.

designTree: Compute a design matrix or non-negative LS

dfactorial: Arithmetic Operators

distanceHadamard: Distance Hadamard

dist.hamming: Pairwise Distances from Sequences

dist.p: Pairwise Polymorphism P-Distances from DNA Sequences

getClans: Clans, slices and clips

hadamard: Hadamard Matrices and Fast Hadamard Multiplication

Laurasiatherian: Laurasiatherian data (AWCMEE)

lento: Lento plot

maxCladeCred: Maximum clade credibility tree

midpoint: Tree manipulation

modelTest: ModelTest

neighborNet: Computes a neighborNet from a distance matrix

NJ: Neighbor-Joining

nni: Tree rearrangements.

parsimony: Parsimony tree.

phangorn-package: Phylogenetic analysis in R

phyDat: Conversion among Sequence Formats

pml: Likelihood of a tree.

pmlCluster: Stochastic Partitioning

pml.fit: Internal maximum likelihood functions.

pmlMix: Phylogenetic mixture model

pmlPart: Partition model.

read.aa: Read Amino Acid Sequences in a File

read.nexus.splits: Function to import and export splits and networks

SH.test: Shimodaira-Hasegawa Test

simSeq: Simulate sequences.

SOWH.test: Swofford-Olsen-Waddell-Hillis Test

splitsNetwork: Phylogenetic Network

superTree: Super Tree methods

treedist: Distances between trees

upgma: UPGMA and WPGMA

writeDist: Writing and reading distances in phylip and nexus format

yeast: Yeast alignment (Rokas et al.)

Functions

acctran Man page
acgt2ry Man page
addConfidences Man page
addTrivialSplits Man page
AICc Man page
allCircularSplits Man page
allSitePattern Man page
allSplits Man page
allTrees Man page
Ancestors Man page
ancestral.pars Man page
ancestral.pml Man page
as.AAbin.phyDat Man page
as.bitsplits.splits Man page
as.character.phyDat Man page
as.data.frame.phyDat Man page
as.DNAbin.phyDat Man page
as.Matrix Man page
as.matrix.splits Man page
as.Matrix.splits Man page
as.MultipleAlignment Man page
as.MultipleAlignment.phyDat Man page
as.networx Man page
as.networx.phylo Man page
as.networx.splits Man page
as.phyDat Man page
as.phyDat.alignment Man page
as.phyDat.character Man page
as.phyDat.data.frame Man page
as.phyDat.DNAbin Man page
as.phyDat.factor Man page
as.phyDat.matrix Man page
as.phyDat.MultipleAlignment Man page
as.phylo.splits Man page
as.prop.part.splits Man page
as.splits Man page
as.splits.multiPhylo Man page
as.splits.networx Man page
as.splits.phylo Man page
bab Man page
baseFreq Man page
bootstrap.phyDat Man page
bootstrap.pml Man page
BranchAndBound Man page
cbind.phyDat Man page
Children Man page
chloroplast Man page
CI Man page
cladePar Man page
coalSpeciesTree Man page
codon2dna Man page
compatible Man page
consensusNet Man page
cophenetic.networx Man page
cophenetic.splits Man page
c.phyDat Man page
createLabel Man page
c.splits Man page
delta.score Man page
densiTree Man page
Descendants Man page
designSplits Man page
designTree Man page
dfactorial Man page
discrete.gamma Man page
distanceHadamard Man page
dist.hamming Man page
distinct.splits Man page
dist.logDet Man page
dist.ml Man page
dist.p Man page
diversity Man page
dna2codon Man page
edQt Man page
fhm Man page
fitch Man page
genlight2phyDat Man page
getClans Man page
getClips Man page
getDiversity Man page
getRoot Man page
getSlices Man page
h2st Man page
h4st Man page
hadamard Man page
image.phyDat Man page
KF.dist Man page
Laurasiatherian Man page
ldfactorial Man page
lento Man page
lli Man page
matchSplits Man page
maxCladeCred Man page
midpoint Man page
midpoint.multiPhylo Man page
midpoint.phylo Man page
modelTest Man page
mrca.phylo Man page
multiphyDat2pmlPart Man page
neighborNet Man page
networx Man page
NJ Man page
nni Man page
nnls.networx Man page
nnls.phylo Man page
nnls.splits Man page
nnls.tree Man page
optim.parsimony Man page
optim.pml Man page
pace Man page
parsimony Man page
path.dist Man page
phangorn Man page
phangorn-package Man page
phyDat Man page
phyDat2alignment Man page
phyDat2MultipleAlignment Man page
plotAnc Man page
plotBS Man page
plot.networx Man page
pml Man page
pmlCluster Man page
pml.control Man page
pml.fit Man page
pml.free Man page
pml.init Man page
pmlMix Man page
pmlPart Man page
pmlPart2multiPhylo Man page
pmlPen Man page
PNJ Man page
pratchet Man page
presenceAbsence Man page
print.splits Man page
pruneTree Man page
random.addition Man page
read.aa Man page
readDist Man page
read.nexus.networx Man page
read.nexus.splits Man page
read.phyDat Man page
removeTrivialSplits Man page
removeUndeterminedSites Man page
RF.dist Man page
RI Man page
rNNI Man page
rSPR Man page
sankoff Man page
SH.test Man page
Siblings Man page
simSeq Man page
simSeq.phylo Man page
simSeq.pml Man page
SOWH.test Man page
splits Man page
splitsNetwork Man page
sprdist Man page
SPR.dist Man page
subset.phyDat Man page
superTree Man page
treedist Man page
unique.phyDat Man page
unique.splits Man page
UNJ Man page
upgma Man page
wpgma Man page
wRF.dist Man page
writeDist Man page
write.nexus.dist Man page
write.nexus.networx Man page
write.nexus.splits Man page
write.phyDat Man page
write.splits Man page
yeast Man page

Files

inst
inst/CITATION
inst/README
inst/extdata
inst/extdata/Blosum62.dat
inst/extdata/RtREV.dat
inst/extdata/MtZoa.dat
inst/extdata/wag.dat
inst/extdata/jtt-dcmut.dat
inst/extdata/HIVw.dat
inst/extdata/VT.dat
inst/extdata/mtArt.dat
inst/extdata/HIVb.dat
inst/extdata/mtREV24.dat
inst/extdata/trees
inst/extdata/trees/RAxML_bestTree.3moles
inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
inst/extdata/trees/RAxML_bootstrap.mtG
inst/extdata/trees/woodmouse.mrbayes.nex.con
inst/extdata/trees/Splits.txt
inst/extdata/trees/woodmouse.nxs
inst/extdata/trees/RAxML_bootstrap.3moles
inst/extdata/trees/RAxML_bestTree.Wang.out
inst/extdata/trees/RAxML_bootstrap.AIs
inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
inst/extdata/trees/RAxML_bestTree.YCh
inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
inst/extdata/trees/RAxML_bestTree.AIs
inst/extdata/trees/RAxML_bipartitions.woodmouse
inst/extdata/trees/RAxML_bestTree.mtG
inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
inst/extdata/trees/RAxML_bipartitions.YCh
inst/extdata/trees/RAxML_bipartitions.mtG
inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
inst/extdata/trees/RAxML_bipartitions.3moles
inst/extdata/trees/RAxML_bootstrap.YCh
inst/extdata/trees/RAxML_bootstrap.Wang.out
inst/extdata/trees/primates.dna
inst/extdata/trees/RAxML_bootstrap.woodmouse
inst/extdata/trees/RAxML_bipartitions.AIs
inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
inst/extdata/trees/woodmouse.fasta
inst/extdata/trees/RAxML_distances.Wang.nxs
inst/extdata/FLU.dat
inst/extdata/Dayhoff.dat
inst/extdata/cpREV.dat
inst/extdata/mtmam.dat
inst/extdata/lg.dat
inst/extdata/JTT.dat
inst/extdata/dayhoff-dcmut.dat
inst/doc
inst/doc/Trees.pdf
inst/doc/Networx.R
inst/doc/Trees.Rnw
inst/doc/phangorn-specials.R
inst/doc/Networx.html
inst/doc/IntertwiningTreesAndNetworks.html
inst/doc/IntertwiningTreesAndNetworks.Rmd
inst/doc/Ancestral.pdf
inst/doc/Ancestral.Rnw
inst/doc/phangorn-specials.Rnw
inst/doc/Networx.Rmd
inst/doc/phangorn-specials.pdf
inst/doc/Ancestral.R inst/doc/IntertwiningTreesAndNetworks.R inst/doc/Trees.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test_superTree.R tests/testthat/test_treeManipulation.R tests/testthat/test_treedist.R tests/testthat/test_distances.R tests/testthat/test_pmlPart.R tests/testthat/test_dist_tree.R tests/testthat/test_pml.R tests/testthat/test_hadamard.R tests/testthat/test_splits.R tests/testthat/test_phyDat.R tests/testthat/test_parsimony.R
src
src/Makevars
src/fitch.c
src/phangorn_help.cpp
src/read_aa.c
src/registerDynamicSymbol.c
src/sprdist.c
src/sankoff.c
src/ml.c
src/RcppExports.cpp
src/phangorn.c
src/dist.c
NAMESPACE
NEWS
data
data/yeast.RData
data/Laurasiatherian.RData
data/chloroplast.RData
R
R/distSeq.R R/clanistic.R R/cladePar.R R/hadamard.R R/bootstrap.R R/lento.R R/ancestral_pml.R R/modelTest.R R/read.nexus.splits.R R/SH.R R/superTree.R
R/sysdata.rda
R/treedist.R R/phangorn-package.R R/pmlPart.R R/distTree.R R/SOWH.R R/splits.R R/phylo.R R/RcppExports.R R/neighborNet.R R/Densi.R R/networx.R R/delta.score.R R/phyDat.R R/fitch.R R/pmlMix.R R/sankoff.R R/Coalescent.R R/simSeq.R R/treeManipulation.R R/dist.p.R R/zzz.R R/parsimony.R
vignettes
vignettes/phangorn.bib
vignettes/Trees.Rnw
vignettes/Trees.RData
vignettes/exdna.txt
vignettes/IntertwiningTreesAndNetworks.Rmd
vignettes/Ancestral.Rnw
vignettes/phangorn-specials.Rnw
vignettes/Networx.Rmd
vignettes/cophylo.png
vignettes/movie.gif
vignettes/primates.dna
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/Laurasiatherian.Rd man/cophenetic.networx.Rd man/addConfidences.Rd man/writeDist.Rd man/dist.p.Rd man/phangorn-package.Rd man/SOWH.test.Rd man/pml.Rd man/neighborNet.Rd man/midpoint.Rd man/coalSpeciesTree.Rd man/splitsNetwork.Rd man/phyDat.Rd man/bab.Rd man/designTree.Rd man/densiTree.Rd man/nni.Rd man/hadamard.Rd man/dist.hamming.Rd man/allTrees.Rd man/parsimony.Rd man/delta.score.Rd man/distanceHadamard.Rd man/consensusNet.Rd man/superTree.Rd man/upgma.Rd man/SH.test.Rd man/lento.Rd man/pmlMix.Rd man/ancestral.pml.Rd man/as.networx.Rd man/dfactorial.Rd man/CI.Rd man/treedist.Rd man/modelTest.Rd man/simSeq.Rd man/bootstrap.pml.Rd man/yeast.Rd man/NJ.Rd man/as.splits.Rd man/pml.fit.Rd man/chloroplast.Rd man/maxCladeCred.Rd man/Ancestors.Rd man/read.nexus.splits.Rd man/cladePar.Rd man/getClans.Rd man/pmlCluster.Rd man/read.aa.Rd man/pmlPart.Rd

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