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.

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 publication2016-12-04 11:42:04
MaintainerKlaus Schliep <klaus.schliep@gmail.com>
LicenseGPL (>= 2)
Version2.1.1
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.splits: Splits representation of graphs and trees.

bab: Branch and bound for finding all most parsimonious trees

bootstrap.pml: Bootstrap

chloroplast: Chloroplast alignment

cladePar: Utility function to plot.phylo

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

plot.networx: Phylogenetic networks

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

SH.test: Shimodaira-Hasegawa Test

simSeq: Simulate sequences.

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

splitsNetwork: Phylogenetic Network

superTree: Super Tree and Species Tree methods

treedist: Distances between trees

upgma: UPGMA and WPGMA

yeast: Yeast alignment (Rokas et al.)

Files in this package

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

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