Files in phangorn
Phylogenetic Reconstruction and Analysis
MD5
NEWS
README.md
NAMESPACE
DESCRIPTION
TODO
R/RcppExports.R
R/sysdata.rda
R/mast.R
R/hash_phylo.R
R/distSeq.R
R/hadamard.R
R/phyDat_conversion.R
R/read.nexus.splits.R
R/discrete.gamma.R
R/dist.p.R
R/pml_control.R
R/pmlPen.R
R/codon.R
R/transferBootstrap.R
R/codonTest.R
R/treeManipulation.R
R/maxCladeCred.R
R/networx.R
R/clanistic.R
R/delta.score.R
R/pml_bb.R
R/F3X4.R
R/addConfidences.R
R/pmlMix.R
R/lento.R
R/pml_generics.R
R/modelTest.R
R/splits.R
R/SOWH.R
R/phangorn-package.R
R/phyDat.R
R/read.phyDat.R
R/Densi.R
R/treedist.R
R/splitsNetwork.R
R/phylo.R
R/image_phyDat.R
R/treeRearrangement.R
R/bootstrap.R
R/distTree.R
R/SH.R
R/neighborNet.R
R/zzz.R
R/draw_CI.R
R/candidate_tree.R
R/bipart.R
R/Coalescent.R
R/superTree.R
R/parsimony.R
R/phyDat2.R
R/baseFreq.R
R/pmlPart.R
R/fitch64.R
R/sankoff.R
R/cladePar.R
R/bab.R
R/simSeq.R
R/ancestral_pml.R
src/Makevars
src/phangorn_utils.cpp
src/phangorn.c
src/RcppExports.cpp
src/phangorn_utils.h
src/sprdist.c
src/dupAtomMat.cpp
src/Fitch.h
src/fitch64.cpp
src/sankoff.c
src/rcSet.h
src/dist.c
src/lessAndEqual.h
src/ml.c
inst/README
inst/CITATION
inst/doc/Trees.Rmd
inst/doc/MLbyHand.html
inst/doc/IntertwiningTreesAndNetworks.R
inst/doc/Morphological.html
inst/doc/Trees.html
inst/doc/Ancestral.Rmd
inst/doc/IntertwiningTreesAndNetworks.html
inst/doc/AdvancedFeatures.html
inst/doc/MLbyHand.Rmd
inst/doc/Networx.R
inst/doc/Trees.R
inst/doc/AdvancedFeatures.Rmd
inst/doc/AdvancedFeatures.R
inst/doc/Morphological.R
inst/doc/Ancestral.R
inst/doc/Morphological.Rmd
inst/doc/Networx.html
inst/doc/Ancestral.html
inst/doc/Networx.Rmd
inst/doc/MLbyHand.R
inst/doc/IntertwiningTreesAndNetworks.Rmd
inst/extdata/VT.dat
inst/extdata/HIVb.dat
inst/extdata/mtREV24.dat
inst/extdata/Dayhoff.dat
inst/extdata/FLU.dat
inst/extdata/jtt-dcmut.dat
inst/extdata/HIVw.dat
inst/extdata/RtREV.dat
inst/extdata/mtArt.dat
inst/extdata/lg.dat
inst/extdata/MtZoa.dat
inst/extdata/mtmam.dat
inst/extdata/cpREV.dat
inst/extdata/JTT.dat
inst/extdata/mites.csv
inst/extdata/mites.nex
inst/extdata/Blosum62.dat
inst/extdata/wag.dat
inst/extdata/dayhoff-dcmut.dat
inst/extdata/trees/RAxML_bootstrap.AIs
inst/extdata/trees/RAxML_distances.Wang.nxs
inst/extdata/trees/RAxML_bipartitions.3moles
inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
inst/extdata/trees/RAxML_bootstrap.YCh
inst/extdata/trees/woodmouse.nxs
inst/extdata/trees/RAxML_bipartitions.YCh
inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
inst/extdata/trees/woodmouse.fasta
inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
inst/extdata/trees/RAxML_bipartitions.mtG
inst/extdata/trees/H3N2_NA_20.fasta
inst/extdata/trees/tree.txt
inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
inst/extdata/trees/woodmouse.mrbayes.nex.con
inst/extdata/trees/primates.dna
inst/extdata/trees/seqfile.txt
inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
inst/extdata/trees/RAxML_bestTree.YCh
inst/extdata/trees/RAxML_bootstrap.Wang.out
inst/extdata/trees/RAxML_bestTree.Wang.out
inst/extdata/trees/Splits.txt
inst/extdata/trees/RAxML_bestTree.mtG
inst/extdata/trees/RAxML_bootstrap.woodmouse
inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
inst/extdata/trees/RAxML_bootstrap.mtG
inst/extdata/trees/RAxML_bestTree.AIs
inst/extdata/trees/RAxML_bestTree.3moles
inst/extdata/trees/RAxML_bipartitions.woodmouse
inst/extdata/trees/H3N2_NA_20.csv
inst/extdata/trees/RAxML_bipartitions.AIs
inst/extdata/trees/RAxML_bootstrap.3moles
inst/tinytest/test_hash.R
inst/tinytest/test_SH.R
inst/tinytest/test_superTree.R
inst/tinytest/test_mast.R
inst/tinytest/test_phyDat.R
inst/tinytest/test_pmlCluster.R
inst/tinytest/test_hadamard.R
inst/tinytest/test_Clanistics.R
inst/tinytest/test_pmlPart.R
inst/tinytest/test_distances.R
inst/tinytest/test_codon.R
inst/tinytest/test_parsimony.R
inst/tinytest/test_pmlMix.R
inst/tinytest/test_pml.R
inst/tinytest/test_speciesTree.R
inst/tinytest/test_candidate_tree.R
inst/tinytest/test_pml_generics.R
inst/tinytest/test_treeManipulation.R
inst/tinytest/test_bootstrap.R
inst/tinytest/test_dist_tree.R
inst/tinytest/test_treedist.R
inst/tinytest/test_ancestral.R
inst/tinytest/test_pmlPen.R
inst/tinytest/test_splits.R
inst/tinytest/test_treeRearrangement.R
inst/tinytest/test_modelTest.R
build/vignette.rds
tests/tinytest.R
vignettes/Trees.Rmd
vignettes/seqLogo.png
vignettes/movie.gif
vignettes/Ancestral.Rmd
vignettes/MLbyHand.Rmd
vignettes/AdvancedFeatures.Rmd
vignettes/phangorn.bib
vignettes/Morphological.Rmd
vignettes/cophylo.png
vignettes/AF.RData
vignettes/Trees.RData
vignettes/Networx.Rmd
vignettes/IntertwiningTreesAndNetworks.Rmd
data/mites.RData
data/yeast.RData
data/chloroplast.RData
data/Laurasiatherian.RData
man/read.aa.Rd
man/dist.hamming.Rd
man/codonTest.Rd
man/midpoint.Rd
man/nni.Rd
man/dfactorial.Rd
man/mast.Rd
man/dist.p.Rd
man/chloroplast.Rd
man/superTree.Rd
man/delta.score.Rd
man/phangorn-internal.Rd
man/neighborNet.Rd
man/Laurasiatherian.Rd
man/reexports.Rd
man/as.splits.Rd
man/as.phyDat.Rd
man/yeast.Rd
man/transferBootstrap.Rd
man/cladePar.Rd
man/pml.Rd
man/baseFreq.Rd
man/simSeq.Rd
man/treedist.Rd
man/writeDist.Rd
man/phangorn-package.Rd
man/image.phyDat.Rd
man/distanceHadamard.Rd
man/SH.test.Rd
man/add_edge_length.Rd
man/ancestral.pml.Rd
man/modelTest.Rd
man/identify.networx.Rd
man/upgma.Rd
man/pmlCluster.Rd
man/phyDat.Rd
man/parsimony.Rd
man/hadamard.Rd
man/read.phyDat.Rd
man/coalSpeciesTree.Rd
man/densiTree.Rd
man/add_ci.Rd
man/NJ.Rd
man/pmlMix.Rd
man/consensusNet.Rd
man/bootstrap.pml.Rd
man/pml_bb.Rd
man/designTree.Rd
man/SOWH.test.Rd
man/getClans.Rd
man/add.tips.Rd
man/addConfidences.Rd
man/mites.Rd
man/read.nexus.splits.Rd
man/discrete.gamma.Rd
man/pml.control.Rd
man/dna2codon.Rd
man/CI.Rd
man/pml.fit.Rd
man/allTrees.Rd
man/splitsNetwork.Rd
man/bab.Rd
man/maxCladeCred.Rd
man/Ancestors.Rd
man/lento.Rd
man/plot.networx.Rd
man/cophenetic.networx.Rd
man/as.networx.Rd
man/plotBS.Rd
man/pmlPart.Rd
man/figures/logo.png
man/figures/phangorn_sticker.png
