phangorn: Phylogenetic Analysis in R

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

Author
Klaus 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 publication
2016-12-04 11:42:04
Maintainer
Klaus Schliep <klaus.schliep@gmail.com>
License
GPL (>= 2)
Version
2.1.1
URLs

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