Files in phangorn
Phylogenetic Reconstruction and Analysis

MD5
NEWS
DESCRIPTION
README.md
NAMESPACE
inst/README
inst/CITATION
inst/doc/Ancestral.Rnw
inst/doc/Networx.html
inst/doc/IntertwiningTreesAndNetworks.html
inst/doc/Networx.R
inst/doc/phangorn-specials.Rnw
inst/doc/Ancestral.R inst/doc/IntertwiningTreesAndNetworks.Rmd
inst/doc/Trees.Rnw
inst/doc/Ancestral.pdf inst/doc/Trees.pdf inst/doc/IntertwiningTreesAndNetworks.R inst/doc/phangorn-specials.R inst/doc/Networx.Rmd inst/doc/Trees.R inst/doc/phangorn-specials.pdf
inst/extdata/MtZoa.dat
inst/extdata/wag.dat
inst/extdata/mtmam.dat
inst/extdata/Blosum62.dat
inst/extdata/dayhoff-dcmut.dat
inst/extdata/HIVb.dat
inst/extdata/JTT.dat
inst/extdata/mtArt.dat
inst/extdata/jtt-dcmut.dat
inst/extdata/mtREV24.dat
inst/extdata/VT.dat
inst/extdata/cpREV.dat
inst/extdata/FLU.dat
inst/extdata/lg.dat
inst/extdata/Dayhoff.dat
inst/extdata/HIVw.dat
inst/extdata/RtREV.dat
inst/extdata/trees/RAxML_bipartitions.YCh
inst/extdata/trees/RAxML_bootstrap.Wang.out
inst/extdata/trees/Splits.txt
inst/extdata/trees/RAxML_distances.Wang.nxs
inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
inst/extdata/trees/RAxML_bestTree.AIs
inst/extdata/trees/woodmouse.nxs
inst/extdata/trees/RAxML_bootstrap.mtG
inst/extdata/trees/primates.dna
inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
inst/extdata/trees/RAxML_bipartitions.AIs
inst/extdata/trees/woodmouse.fasta
inst/extdata/trees/RAxML_bestTree.mtG
inst/extdata/trees/RAxML_bootstrap.YCh
inst/extdata/trees/RAxML_bootstrap.AIs
inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
inst/extdata/trees/RAxML_bestTree.Wang.out
inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
inst/extdata/trees/RAxML_bestTree.YCh
inst/extdata/trees/RAxML_bestTree.3moles
inst/extdata/trees/RAxML_bipartitions.3moles
inst/extdata/trees/RAxML_bootstrap.3moles
inst/extdata/trees/RAxML_bootstrap.woodmouse
inst/extdata/trees/woodmouse.mrbayes.nex.con
inst/extdata/trees/RAxML_bipartitions.mtG
inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
inst/extdata/trees/RAxML_bipartitions.woodmouse
vignettes/phangorn.bib
vignettes/Ancestral.Rnw
vignettes/cophylo.png
vignettes/primates.dna
vignettes/exdna.txt
vignettes/phangorn-specials.Rnw
vignettes/IntertwiningTreesAndNetworks.Rmd
vignettes/movie.gif
vignettes/Trees.Rnw
vignettes/seqLogo.pdf vignettes/Networx.Rmd
vignettes/Trees.RData
R/lento.R R/treedist.R R/zzz.R R/read.nexus.splits.R R/SH.R R/Densi.R R/simSeq.R R/pmlPart.R R/cladePar.R R/phyDat.R R/bootstrap.R R/distTree.R R/networx.R R/SOWH.R R/dist.p.R R/RcppExports.R R/fitch.R R/phangorn-package.R R/neighborNet.R R/treeRearrangement.R R/parsimony.R R/pmlPen.R R/Coalescent.R R/phylo.R
R/sysdata.rda
R/ancestral_pml.R R/splits.R R/hadamard.R R/superTree.R R/pmlMix.R R/distSeq.R R/treeManipulation.R R/clanistic.R R/sankoff.R R/delta.score.R R/mast.R R/modelTest.R
src/dist.c
src/ml.c
src/init.c
src/ancThresh.cpp
src/RcppExports.cpp
src/fitch.c
src/phangorn_help.cpp
src/read_aa.c
src/sprdist.c
src/phangorn.c
src/sankoff.c
src/Makevars
man/pml.Rd man/hadamard.Rd man/midpoint.Rd man/lento.Rd man/phyDat.Rd man/designTree.Rd man/nni.Rd man/bootstrap.pml.Rd man/dfactorial.Rd man/dist.p.Rd man/NJ.Rd man/pmlMix.Rd man/SOWH.test.Rd man/neighborNet.Rd man/delta.score.Rd man/distanceHadamard.Rd man/identify.networx.Rd man/parsimony.Rd man/superTree.Rd man/cladePar.Rd man/ancestral.pml.Rd man/SH.test.Rd man/coalSpeciesTree.Rd man/getClans.Rd man/bab.Rd man/pmlPart.Rd man/CI.Rd man/dist.hamming.Rd man/add.tips.Rd man/upgma.Rd man/as.splits.Rd man/Ancestors.Rd man/mast.Rd man/allTrees.Rd man/simSeq.Rd man/addConfidences.Rd man/consensusNet.Rd man/read.aa.Rd man/phangorn-package.Rd man/splitsNetwork.Rd man/phangorn-internal.Rd man/treedist.Rd man/pmlCluster.Rd man/yeast.Rd man/densiTree.Rd man/writeDist.Rd man/cophenetic.networx.Rd man/as.networx.Rd man/read.nexus.splits.Rd man/maxCladeCred.Rd man/pml.fit.Rd man/chloroplast.Rd man/modelTest.Rd man/Laurasiatherian.Rd
build/vignette.rds
tests/testthat.R tests/testthat/test_speciesTree.R tests/testthat/test_superTree.R tests/testthat/test_pmlPart.R tests/testthat/test_pmlPen.R tests/testthat/test_pml.R tests/testthat/test_treedist.R tests/testthat/test_ancestral.R tests/testthat/test_splits.R tests/testthat/test_pmlCluster.R tests/testthat/test_modelTest.R tests/testthat/test_parsimony.R tests/testthat/test_SH.R tests/testthat/test_phyDat.R tests/testthat/test_treeManipulation.R tests/testthat/test_treeRearrangement.R tests/testthat/test_Clanistics.R tests/testthat/test_hadamard.R tests/testthat/test_dist_tree.R tests/testthat/test_distances.R tests/testthat/test_mast.R tests/testthat/test_pmlMix.R
data/yeast.RData
data/Laurasiatherian.RData
data/chloroplast.RData
phangorn documentation built on Feb. 16, 2018, 1:02 a.m.