Files in YuLab-SMU/treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
.Rbuildignore
.covrignore
.github/CONTRIBUTING.md
.github/issue_template.md
.github/pull_request_template.md
.gitignore
.travis.yml
CONDUCT.md
CONTRIBUTORS.md
DESCRIPTION
Makefile
NAMESPACE
NEWS.md
R/ASTRAL.R
R/AllClasses.R
R/AllGenerics.R
R/MCMCTree.R
R/RAxML.R
R/ape.R
R/beast.R
R/codeml.R
R/codeml_mlc.R
R/hyphy.R
R/iqtree.R
R/jplace.R
R/jtree.R
R/mask.R
R/mega.R
R/merge_tree.R
R/method-as-phylo.R
R/method-as-treedata.R
R/method-spt.R
R/newick.R
R/nextstrain.json.R
R/nhx.R
R/paml.R
R/paml_rst.R
R/phangorn.R
R/phylip.R
R/phyloxml.R
R/print.R
R/r8s.R
R/raxml2nwk.R
R/reexport.R
R/rename.R
R/reroot-utilities.R
R/rescale_tree.R
R/sequence-utilities.R
R/tree-utilities.R
R/treeio-package.R
R/treeqza.R
R/treetime.R
R/utilities.R
R/write-beast.R
R/write-jplace.R
R/zzz.R
README.Rmd
README.md
appveyor.yml
codemeta.json
inst/CITATION
inst/extdata/BEAST/beast_mcc.tree
inst/extdata/EPA.jplace
inst/extdata/HYPHY/ancseq.nex
inst/extdata/HYPHY/labelledtree.tree
inst/extdata/MCMCTree/mcmctree_output.tree
inst/extdata/MEGA7/mtCDNA_timetree.nex
inst/extdata/MEGA7/mtCDNA_timetree.nwk
inst/extdata/MEGA7/mtCDNA_timetree_tabular.txt
inst/extdata/MrBayes/Gq_nxs.tre
inst/extdata/NHX/ADH.nhx
inst/extdata/NHX/compra.nhx
inst/extdata/NHX/notung.nhx
inst/extdata/NHX/phyldog.nhx
inst/extdata/PAML_Baseml/mlb
inst/extdata/PAML_Baseml/rst
inst/extdata/PAML_Codeml/mlc
inst/extdata/PAML_Codeml/rst
inst/extdata/RAxML/Dated_FluA_H3.fas
inst/extdata/RAxML/RAxML_bestTree.H3
inst/extdata/RAxML/RAxML_bipartitions.H3
inst/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3
inst/extdata/RAxML/RAxML_bootstrap.H3
inst/extdata/RAxML/RAxML_info.H3
inst/extdata/nextstrain.json/minimal_v2.json
inst/extdata/pa.fas
inst/extdata/pa.nwk
inst/extdata/pa_subs.csv
inst/extdata/phyloxml/phyloxml_examples.xml
inst/extdata/phyloxml/test_x2.xml
inst/extdata/qiime2treeqza/fasttree-tree.qza
inst/extdata/qiime2treeqza/iqt-tree.qza
inst/extdata/qiime2treeqza/raxml-cat-bootstrap-tree.qza
inst/extdata/qiime2treeqza/raxml-cat-tree.qza
inst/extdata/r8s/H3.r8s
inst/extdata/r8s/H3.tree
inst/extdata/r8s/H3_r8s_output.log
inst/extdata/ref35extend.jplace
inst/extdata/sample.jplace
inst/extdata/sample.nwk
inst/extdata/sample.phy
inst/extdata/twoD.tree
inst/extdata/upwelling.jplace
man/as.treedata.Rd
man/beast-parser.Rd
man/figures/logo.png
man/find.hclust.Rd
man/get-placements.Rd
man/get.tree.Rd
man/get.treetext-methods.Rd
man/getNodeNum.Rd
man/is.ggtree.Rd
man/jplace-class.Rd
man/label_branch_paml.Rd
man/mask.Rd
man/merge_tree.Rd
man/print.treedataList.Rd
man/raxml2nwk.Rd
man/read-jtree.Rd
man/read.astral.Rd
man/read.codeml.Rd
man/read.codeml_mlc.Rd
man/read.fasta.Rd
man/read.hyphy.Rd
man/read.hyphy.seq.Rd
man/read.iqtree.Rd
man/read.jplace.Rd
man/read.mcmctree.Rd
man/read.mega_tabular.Rd
man/read.newick.Rd
man/read.nextstrain.json.Rd
man/read.nhx.Rd
man/read.paml_rst.Rd
man/read.phylip.Rd
man/read.phylip.seq.Rd
man/read.phylip.tree.Rd
man/read.phyloxml.Rd
man/read.r8s.Rd
man/read.raxml.Rd
man/read.treeqza.Rd
man/reexports.Rd
man/rename_taxa.Rd
man/rescale_tree.Rd
man/spt-methods.Rd
man/treeio-package.Rd
man/treetime.Rd
man/write-jtree.Rd
man/write.beast.Rd
man/write.beast.newick.Rd
man/write.jplace.Rd
tests/testthat.R
tests/testthat/test-as-phylo.R
tests/testthat/test-beast.R
tests/testthat/test-conversion.R
tests/testthat/test-jplace.R
tests/testthat/test-jtree.R
tests/testthat/test-merge-tree.R
tests/testthat/test-nhx.R
tests/testthat/test-parser.R
tests/testthat/test-phyloxml.R
tests/testthat/test-r8s.R
tests/testthat/test-spt.R
tests/testthat/test-tree-subset.R
tests/testthat/test-treedata-accessor.R
tests/testthat/test-treeqza.R
tests/testthat/test-utilities.R
treeio.Rproj
vignettes/treeio.Rmd
