Files in treeio

Base Classes and Functions for Phylogenetic Tree Input and Output

NEWS.md

NAMESPACE

DESCRIPTION

README.md tests/testthat.R tests/testthat/test-merge-tree.R tests/testthat/test-nhx.R tests/testthat/test-utilities.R tests/testthat/test-beast.R tests/testthat/test-access-related-nodes.R tests/testthat/test-treedata-accessor.R tests/testthat/test-r8s.R tests/testthat/test-tree-subset.R tests/testthat/test-conversion.R tests/testthat/test-fulljoin.R tests/testthat/test-as-phylo.R tests/testthat/test-jtree.R tests/testthat/test-jplace.R tests/testthat/test-parser.R R/full-join.R R/tree-utilities.R R/ape.R R/beast.R R/raxml2nwk.R R/method-groupClade.R R/rescale_tree.R R/nhx.R R/method-as-tibble.R R/method-as-phylo.R R/AllClasses.R R/method-nodeid.R R/offspring.R R/ancestor.R R/jplace.R R/newick.R R/sequence-utilities.R R/write-beast.R R/r8s.R R/jtree.R R/tree-subset.R R/hyphy.R R/phylip.R R/AllGenerics.R R/codeml.R R/phyloxml.R R/isTip.R R/codeml_mlc.R R/merge_tree.R R/method-drop-tip.R R/RAxML.R R/utilities.R R/reexport.R R/rename.R R/mega.R R/sibling.R R/method-as-treedata.R R/paml_rst.R R/paml.R R/method-reroot.R R/phangorn.R R/print.R R/method-get-treetext.R R/zzz.R R/ASTRAL.R R/method-groupOTU.R R/mask.R R/method-MRCA.R R/iqtree.R man/as.treedata.Rd man/print.treedataList.Rd man/read.phylip.tree.Rd man/read.hyphy.seq.Rd man/read.phyloxml.Rd man/read.phylip.seq.Rd man/get.treetext-methods.Rd man/tree_subset.Rd man/read.fasta.Rd man/drop.tip-methods.Rd man/root-method.Rd man/read.codeml_mlc.Rd man/read.hyphy.Rd man/raxml2nwk.Rd man/read.astral.Rd man/is.ggtree.Rd man/rescale_tree.Rd man/merge_tree.Rd man/beast-parser.Rd man/read-jtree.Rd man/Nnode.treedata.Rd man/read.jplace.Rd man/write-jtree.Rd man/read.raxml.Rd man/get.tree.Rd man/read.paml_rst.Rd man/reexports.Rd man/mask.Rd man/read.iqtree.Rd man/jplace-class.Rd man/read.newick.Rd man/read.r8s.Rd man/read.codeml.Rd man/read.nhx.Rd man/read.phylip.Rd man/getNodeNum.Rd man/get-placements.Rd man/isTip.Rd man/label_branch_paml.Rd man/write.beast.Rd man/read.mega_tabular.Rd man/rename_taxa.Rd

inst/CITATION

inst/extdata/pa.fas

inst/extdata/pa_subs.csv

inst/extdata/pa.nwk

inst/extdata/sample.jplace

inst/extdata/ref35extend.jplace

inst/extdata/EPA.jplace

inst/extdata/upwelling.jplace

inst/extdata/sample.nwk

inst/extdata/sample.phy

inst/extdata/twoD.tree

inst/extdata/MrBayes/Gq_nxs.tre

inst/extdata/RAxML/RAxML_bestTree.H3

inst/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3

inst/extdata/RAxML/RAxML_info.H3

inst/extdata/RAxML/Dated_FluA_H3.fas

inst/extdata/RAxML/RAxML_bootstrap.H3

inst/extdata/RAxML/RAxML_bipartitions.H3

inst/extdata/phyloxml/phyloxml_examples.xml

inst/extdata/phyloxml/test_x2.xml

inst/extdata/r8s/H3_r8s_output.log

inst/extdata/r8s/H3.r8s

inst/extdata/r8s/H3.tree

inst/extdata/PAML_Baseml/rst

inst/extdata/PAML_Baseml/mlb

inst/extdata/NHX/phyldog.nhx

inst/extdata/NHX/compra.nhx

inst/extdata/NHX/ADH.nhx

inst/extdata/NHX/notung.nhx

inst/extdata/HYPHY/ancseq.nex

inst/extdata/HYPHY/labelledtree.tree

inst/extdata/BEAST/beast_mcc.tree

inst/extdata/PAML_Codeml/rst

inst/extdata/PAML_Codeml/mlc

inst/extdata/MEGA7/mtCDNA_timetree.nex

inst/extdata/MEGA7/mtCDNA_timetree.nwk

inst/extdata/MEGA7/mtCDNA_timetree_tabular.txt

inst/doc/treeio.html

inst/doc/treeio.Rmd inst/doc/treeio.R

build/vignette.rds

vignettes/treeio.Rmd

treeio documentation built on Nov. 21, 2020, 2:01 a.m.