Files in KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis

.Rbuildignore

.github/.gitignore

.github/CODE_OF_CONDUCT.md

.github/workflows/R-CMD-check.yaml

.github/workflows/pkgdown.yaml

.github/workflows/recheck.yml

.github/workflows/release-file-system-image.yml

.github/workflows/rhub.yaml

.github/workflows/test-coverage.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/Coalescent.R R/Densi.R R/F3X4.R R/RcppExports.R R/SH.R R/SOWH.R R/addConfidences.R R/ancestral.R R/ancestral_generics.R R/bab.R R/baseFreq.R R/bipart.R R/bootstrap.R R/candidate_tree.R R/cladePar.R R/clanistic.R R/codon.R R/codonTest.R R/consensusNet.R R/delta.score.R R/discrete.gamma.R R/dist.p.R R/distSeq.R R/distTree.R R/draw_CI.R R/fitch64.R R/gap_as_state.R R/hadamard.R R/hash_phylo.R R/image_phyDat.R R/joint_ASR.R R/lento.R R/linkfun.R R/ltg2amb.R R/mast.R R/maxCladeCred.R R/modelTest.R R/neighborNet.R R/networx.R R/parsimony.R R/phangorn-package.R R/phyDat.R R/phyDat2.R R/phyDat_conversion.R R/phylo.R R/plotAnc.R R/plotBS.R R/plot_networx.R R/plot_pml.R R/pmlMix.R R/pmlPart.R R/pmlPen.R R/pml_bb.R R/pml_control.R R/pml_generics.R R/read.nexus.partitions.R R/read.nexus.splits.R R/read.phyDat.R R/sankoff.R R/simSeq.R R/splits.R R/splitsNetwork.R R/superTree.R

R/sysdata.rda

R/transferBootstrap.R R/treeManipulation.R R/treeRearrangement.R R/treedist.R R/upgma.R R/zzz.R README.md

_pkgdown.yml

codecov.yml

data/Laurasiatherian.RData

data/chloroplast.RData

data/mites.RData

data/yeast.RData

inst/CITATION

inst/README

inst/extdata/Blosum62.dat

inst/extdata/Dayhoff.dat

inst/extdata/FLU.dat

inst/extdata/HIVb.dat

inst/extdata/HIVw.dat

inst/extdata/JTT.dat

inst/extdata/MtZoa.dat

inst/extdata/RtREV.dat

inst/extdata/VT.dat

inst/extdata/cpREV.dat

inst/extdata/dayhoff-dcmut.dat

inst/extdata/jtt-dcmut.dat

inst/extdata/lg.dat

inst/extdata/mites.csv

inst/extdata/mites.nex

inst/extdata/mtArt.dat

inst/extdata/mtREV24.dat

inst/extdata/mtmam.dat

inst/extdata/trees/H3N2_NA_20.csv

inst/extdata/trees/H3N2_NA_20.fasta

inst/extdata/trees/RAxML_bestTree.3moles

inst/extdata/trees/RAxML_bestTree.AIs

inst/extdata/trees/RAxML_bestTree.Wang.out

inst/extdata/trees/RAxML_bestTree.YCh

inst/extdata/trees/RAxML_bestTree.mtG

inst/extdata/trees/RAxML_bipartitions.3moles

inst/extdata/trees/RAxML_bipartitions.AIs

inst/extdata/trees/RAxML_bipartitions.YCh

inst/extdata/trees/RAxML_bipartitions.mtG

inst/extdata/trees/RAxML_bipartitions.woodmouse

inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles

inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs

inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh

inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG

inst/extdata/trees/RAxML_bootstrap.3moles

inst/extdata/trees/RAxML_bootstrap.AIs

inst/extdata/trees/RAxML_bootstrap.Wang.out

inst/extdata/trees/RAxML_bootstrap.YCh

inst/extdata/trees/RAxML_bootstrap.mtG

inst/extdata/trees/RAxML_bootstrap.woodmouse

inst/extdata/trees/RAxML_distances.Wang.nxs

inst/extdata/trees/Splits.txt

inst/extdata/trees/primates.dna

inst/extdata/trees/seqfile.txt

inst/extdata/trees/tree.txt

inst/extdata/trees/woodmouse.fasta

inst/extdata/trees/woodmouse.mrbayes.nex.con

inst/extdata/trees/woodmouse.mrbayes.nex.run1.t

inst/extdata/trees/woodmouse.mrbayes.nex.run2.t

inst/extdata/trees/woodmouse.nxs

inst/extdata/wag.dat

man/figures/logo.png

man/figures/phangorn_sticker.png

man/gap_as_state.Rd man/getClans.Rd man/hadamard.Rd man/identify.networx.Rd man/image.phyDat.Rd man/latag2n.phyDat.Rd man/lento.Rd man/mast.Rd man/maxCladeCred.Rd man/midpoint.Rd man/mites.Rd man/modelTest.Rd man/neighborNet.Rd man/nni.Rd man/parsimony.Rd man/phangorn-internal.Rd man/phangorn-package.Rd man/phyDat.Rd man/plot.ancestral.Rd man/plot.networx.Rd man/plot.pml.Rd man/plotBS.Rd man/pml.Rd man/pml.control.Rd man/pml.fit.Rd man/pmlCluster.Rd man/pmlMix.Rd man/pmlPart.Rd man/pml_bb.Rd man/read.nexus.partitions.Rd man/read.nexus.splits.Rd man/read.phyDat.Rd man/reexports.Rd man/simSeq.Rd man/splitsNetwork.Rd man/superTree.Rd man/transferBootstrap.Rd man/treedist.Rd man/upgma.Rd man/write.ancestral.Rd man/write.pml.Rd man/writeDist.Rd man/yeast.Rd

phangorn.Rproj

src/Fitch.h

src/Makevars

src/RcppExports.cpp

src/dist.c

src/dupAtomMat.cpp

src/fitch64.cpp

src/lessAndEqual.h

src/ml.c

src/phangorn.c

src/phangorn_utils.cpp

src/phangorn_utils.h

src/rcSet.h

src/sankoff.c

src/sprdist.c

tests/testthat.R

tests/testthat/_snaps/plot_ancestral/pie-plots.svg

tests/testthat/_snaps/plot_ancestral/seqlogo.svg

tests/testthat/_snaps/plot_networx/plot-networx.svg

tests/testthat/_snaps/plot_pml/densitree.svg

tests/testthat/_snaps/plot_pml/plot-pml.svg

tests/testthat/test_plot_ancestral.R tests/testthat/test_plot_networx.R tests/testthat/test_plot_pml.R tests/tinytest.R

vignettes/AF.RData

vignettes/AdvancedFeatures.Rmd vignettes/Ancestral.Rmd vignettes/IntertwiningTreesAndNetworks.Rmd vignettes/MLbyHand.Rmd vignettes/Morphological.Rmd vignettes/Networx.Rmd

vignettes/Trees.RData

vignettes/Trees.Rmd

vignettes/cophylo.png

vignettes/movie.gif

vignettes/phangorn.bib

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.

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KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis

Files in KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis

R Package Documentation

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KlausVigo/phangorn Phylogenetic Reconstruction and Analysis

Files in KlausVigo/phangorn Phylogenetic Reconstruction and Analysis

R Package Documentation

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We want your feedback!

KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis

Files in KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis