57f35c2567fe9a3e99da9049dc332878 *DESCRIPTION
edc3f7b384c42ea9310b4db1f99efc26 *NAMESPACE
4c50cb6a97011e10bd24e5f29871c05c *NEWS.md
cf80fb67b0ed1f1a7dad231c9d6a61f1 *R/ASTRAL.R
f726cfef07ae995c2ad14a0296fe9d61 *R/AllClasses.R
5d3411dabea6f4f0d66e2792b6516b3a *R/AllGenerics.R
19144080d10fbf2a705924105cd5e120 *R/MCMCTree.R
4bb55ebd5730f59bf4e4c5fca538ecfa *R/RAxML.R
88f37fe9a445dc28e3ce435bb5b3ac63 *R/ape.R
7e397545c912e0f5fa9a892d9ce3e277 *R/beast.R
a29ed9c9ae8e82487942c7b4a5d3a9fe *R/codeml.R
ac24e6de92d702338a1ca1700c3dd9aa *R/codeml_mlc.R
309a180e2b1432c9ff12ffd0d47249e0 *R/hyphy.R
ae89ed5c98eef2bee446fdb48984e757 *R/iqtree.R
4ab66fefc0be16efe42700e31b50165d *R/jplace.R
f6d65e5563a8b0fdc41605b34a31e1a1 *R/jtree.R
dc141df42adbbc050d574138a842829e *R/mask.R
eac0225073bff5b76166a746f382590c *R/mega.R
facce35efee567cc24d6e54d1b3d9b79 *R/merge_tree.R
dba5e69991d01cff2b0bdd04e073a622 *R/method-as-phylo.R
7569aa0e48d8faa42fb9a4cb21610d38 *R/method-as-treedata.R
1048a4008c74d50a32efa493bfe2d0cf *R/method-spt.R
4a1cfc9dd2d742346e8b2d67e3cad72c *R/newick.R
7497e194ce9854de8c968ee820c475f2 *R/nextstrain.json.R
4f3127d0ca257565dd0bc738d51a7e64 *R/nhx.R
4e5ec21ad9fd9055c53aa124e0990179 *R/paml.R
37ce1b70d68c48f3914ca206d866b947 *R/paml_rst.R
440f7f9442a981901cf0144e0310e6c7 *R/phangorn.R
7678cc1047640b46ef1e9040b473558d *R/phylip.R
e410435ed6657c3f4de57edcceee0509 *R/phyloxml.R
2533dc01ffc5181ba59e09ea1420c3d1 *R/print.R
0b8418fd5d38ce2d1d6da3c2d541c5eb *R/r8s.R
c4020792bc23f52a2e3ffb2d710c185c *R/raxml2nwk.R
e5db864aa15625d2c2bc01102ccc9536 *R/reexport.R
b11cfa8c0a9246f42d68fd6e2a5809d6 *R/rename.R
8249bb91d55a5884f75befb4b38b1be2 *R/reroot-utilities.R
d4fd8cb4432dd64126e1f5e3d51464a3 *R/rescale_tree.R
8481c1a4ebbb8d7b7d9bd1363d4d67c5 *R/sequence-utilities.R
3d2778ac59bde44ae8dd5f2c768d7a07 *R/tree-utilities.R
df6cc46bc7fae1a55b713f3d5065b35a *R/treeio-package.R
ac1d02df0874d11a4c7a4d0c1d62d931 *R/treeqza.R
931513877527d798c22a52e9031f4b68 *R/treetime.R
5f646f2113c5876f62bf8eda148378dd *R/utilities.R
7d2575f18d5e3110c4209dfb7664c463 *R/write-beast.R
9815bd2f8ac7dd0c52c7c44dae193d43 *R/write-jplace.R
f04edd212411e75d033f6a1cb5e0e2ce *R/zzz.R
61e482dcb3d92492e252c7c5bb68a11a *README.md
9b4ed6ffb451350fb8df223863c7eaf6 *build/vignette.rds
df48a7425eb32426c40bf06dc995847d *inst/CITATION
b51c42c5cd26de1d0bc4f1f3b72a805d *inst/doc/treeio.R
39f1cc80ac4ad97deb86ec9cac26cde3 *inst/doc/treeio.Rmd
9daabeffad91a45b1dcc2d71ac89c5f2 *inst/doc/treeio.html
68cbc1ad334aa4f61b51a5122a035bbd *inst/extdata/BEAST/beast_mcc.tree
b7f373a3687789010098ca33a2fb2800 *inst/extdata/EPA.jplace
d6623cc693865d91d91a2fb21d515150 *inst/extdata/HYPHY/ancseq.nex
e4a728157b3b05732ec462ef94faa868 *inst/extdata/HYPHY/labelledtree.tree
c51c7e6df6b66f20fb0570ae3a894138 *inst/extdata/MCMCTree/mcmctree_output.tree
7b6ebd898e270401f2ded1900f14c161 *inst/extdata/MEGA7/mtCDNA_timetree.nex
d0218afc0b609c37dbf14f73539b92bd *inst/extdata/MEGA7/mtCDNA_timetree.nwk
fa2b00e54682c5ade008b6b3ab208292 *inst/extdata/MEGA7/mtCDNA_timetree_tabular.txt
88f88b3f0c3c416e6766f94476d0025f *inst/extdata/MrBayes/Gq_nxs.tre
4131b4705e1c1285c5520261074466d8 *inst/extdata/NHX/ADH.nhx
82c0ac1b3d3083ce8a25a86dbf70f6f6 *inst/extdata/NHX/compra.nhx
980a45ad1b29fe2109bc67dadbd30fde *inst/extdata/NHX/notung.nhx
9a2a974ff7dce708ba1700d73d267697 *inst/extdata/NHX/phyldog.nhx
8d5005486fedea921944ee154376cad3 *inst/extdata/PAML_Baseml/mlb
9a5dc7ed0a29baea6f82fed014d3eab7 *inst/extdata/PAML_Baseml/rst
5868cbe7dfbd6e22bfd7573e9cb48315 *inst/extdata/PAML_Codeml/mlc
8633c5ea8677ac8e270796ec1a7a5b15 *inst/extdata/PAML_Codeml/rst
d38c669af65f71130dffe9d49dba9740 *inst/extdata/RAxML/Dated_FluA_H3.fas
278537cf999a7c956c9cfb66362ec2b5 *inst/extdata/RAxML/RAxML_bestTree.H3
4ab09a47105b76100a0ca97afd1238c6 *inst/extdata/RAxML/RAxML_bipartitions.H3
e3ca393b670ba99564ce032e2d45e3f0 *inst/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3
317be8455bec9b1122f2e76d71990560 *inst/extdata/RAxML/RAxML_bootstrap.H3
fda21d972254c933174c90c989faeaee *inst/extdata/RAxML/RAxML_info.H3
9dafc196073a34ad28f5c15b600ef926 *inst/extdata/nextstrain.json/minimal_v2.json
e08daeb982c702c7e5de437c4bf30b3a *inst/extdata/pa.fas
1cea134a8f1922c5138712e2efcbcfa2 *inst/extdata/pa.nwk
2ccc55865e87faa43b3f6f02e0274a2a *inst/extdata/pa_subs.csv
58ebd89aff92fb0d5880a51bc9f9dd18 *inst/extdata/phyloxml/phyloxml_examples.xml
a8f2368ad8c071988b659a04244e574f *inst/extdata/phyloxml/test_x2.xml
c862b925b5ba10e0a411cf197813ba19 *inst/extdata/qiime2treeqza/fasttree-tree.qza
438a009b33acf0e871c9c802e456f003 *inst/extdata/qiime2treeqza/iqt-tree.qza
4c0d9f0d0090e3594a8667519f74685d *inst/extdata/qiime2treeqza/raxml-cat-bootstrap-tree.qza
4e306f31fdd70c67203de255576daf58 *inst/extdata/qiime2treeqza/raxml-cat-tree.qza
1fde7911e63579018236a4b6c0d53c37 *inst/extdata/r8s/H3.r8s
ba130fc5144b6160f808049bf2c8ed08 *inst/extdata/r8s/H3.tree
da34cd5fd6319f53ff7818b5db464602 *inst/extdata/r8s/H3_r8s_output.log
94410aae59d0f302054a47697eae2639 *inst/extdata/ref35extend.jplace
1986759e58325f24fcf4a15447520684 *inst/extdata/sample.jplace
7444c5e18e689ea0f0ef627cdeac9181 *inst/extdata/sample.nwk
cf4acf7a4b905598a716f0944693535e *inst/extdata/sample.phy
d0fa1c43acd64281e90d31c1aea6226b *inst/extdata/twoD.tree
f9d0385d389e96c5b92f691df101793e *inst/extdata/upwelling.jplace
2774d05dd63980399808cddb23e6d944 *man/as.treedata.Rd
36d4ce3889e5cc308318985eb6a42645 *man/beast-parser.Rd
24f1ef905d4dfff93f3287acd6577b58 *man/figures/logo.png
cfa21c974a776ca20e545301bf989f29 *man/find.hclust.Rd
90238fd48a578f2d0e082e10bf81c800 *man/get-placements.Rd
245331a823b9246e79150c19a29eaf95 *man/get.tree.Rd
230052eb84634a603c9a4fa634313ada *man/get.treetext-methods.Rd
7e66a3042f58cb8b9ea8b2e67651ddc7 *man/getNodeNum.Rd
fd09bdb8eafbd257d54f270f8550f0c4 *man/is.ggtree.Rd
cd8c50d3388ad44e50d11817f52286a8 *man/jplace-class.Rd
2a517c80da384c329f43330ad07032b3 *man/label_branch_paml.Rd
364515885ff9f5991a211263e97cbde7 *man/mask.Rd
31cd771a5e376d184c18172ce7f5cf0d *man/merge_tree.Rd
ae4c0a6d1be9fe3f2f490dd35ab67b47 *man/print.treedataList.Rd
8a17e25dcf541a6469486986ed8ced78 *man/raxml2nwk.Rd
133af2be819970ea13ba74366c73f777 *man/read-jtree.Rd
601b5ba785112af0bcea8f783c82aa4e *man/read.astral.Rd
c1c3376874fe8efca3113a3e8165b0ea *man/read.codeml.Rd
fe4a5ee1ceab3d357e5f935a7337003c *man/read.codeml_mlc.Rd
ca6c4f9d2c2c70d3227fe5cc1b0af368 *man/read.fasta.Rd
7bd6076d34012d6a90a482efdcff8750 *man/read.hyphy.Rd
ecce0917c47373e1dff7ec390c197743 *man/read.hyphy.seq.Rd
517238bfb36a0dad10fe94bfa6aff144 *man/read.iqtree.Rd
e7639acc213044df19df00fadb2658e5 *man/read.jplace.Rd
ddc4b3ac7a565d4ba14bdb73e6317aa0 *man/read.mcmctree.Rd
c6e5587086692f0d962fba3b1fd2d2db *man/read.mega_tabular.Rd
9d8507650e52850b7b8c51a7c0b3bf47 *man/read.newick.Rd
a4add63528ba4b395391d9b81807a6e4 *man/read.nextstrain.json.Rd
4ebbe54a5da1478824d5c126bde6024e *man/read.nhx.Rd
60b805edaeb35142ac83d64f4555bbad *man/read.paml_rst.Rd
7ae801a94b213fd1d8ccee59f854648f *man/read.phylip.Rd
046af0e1e20ecc5d074ad799abeca2e9 *man/read.phylip.seq.Rd
327ce18a90ed2d69bf50fb19eabd58d6 *man/read.phylip.tree.Rd
a4dfdd6b30db3deda88c6cf5f2e80366 *man/read.phyloxml.Rd
14369ecacaf76682d64857500cb19f5a *man/read.r8s.Rd
d4b750837f5da55bbbde11a5dfb7632e *man/read.raxml.Rd
c002cdbe2f21ad85e4c13b49d3ebdec5 *man/read.treeqza.Rd
9562f7e557730ceef6df590258b27cfe *man/reexports.Rd
d3ffa62334ed4d672289cf6d46e359b2 *man/rename_taxa.Rd
3f975ceb809ff6f475d63bd2038eb3b5 *man/rescale_tree.Rd
e8929d79e122ceb7baa950040381bf95 *man/spt-methods.Rd
07855d46826b5593d5be7fab2899ce61 *man/treeio-package.Rd
f9c0056796418618ce33cdd392068262 *man/treetime.Rd
357ee3fe2a4e6cc0774f018aae6dbc5f *man/write-jtree.Rd
651ceb06eb8948de782f9a79740ab835 *man/write.beast.Rd
5d6c277dc41eed1aef77609cca195473 *man/write.beast.newick.Rd
3acc0b5b4a40b90eed0a2232d9b5e046 *man/write.jplace.Rd
ed75b1a6c75668772213cb5ef187b6f5 *tests/testthat.R
375205bed94181ee5c6299734dfbda4f *tests/testthat/test-as-phylo.R
603489b120fc6fa00ec5c3fd6888d817 *tests/testthat/test-beast.R
23028973951260594903433717ea910b *tests/testthat/test-conversion.R
d2542588fc83a2f715ac6f3d2fbbba10 *tests/testthat/test-jplace.R
528133d63229edd0078d0e7745aeb5cb *tests/testthat/test-jtree.R
8d1578c809d01b03daf92392853842e5 *tests/testthat/test-merge-tree.R
ae7ba61c95372ffc0144409d24afb2f7 *tests/testthat/test-nhx.R
879eab97ecd070a183d93bd2ac71d7be *tests/testthat/test-parser.R
edbb49c43aed75d092b9518e6bf5f547 *tests/testthat/test-phyloxml.R
8b93d3d98360b713ca7655b57f3566db *tests/testthat/test-r8s.R
9fdac58af92a0351902392deed28bb90 *tests/testthat/test-spt.R
2ba79c2f8bcdecafae4fefb42971824d *tests/testthat/test-tree-subset.R
73aa98e8691423ef106557a90547ebd3 *tests/testthat/test-treedata-accessor.R
5a0782f60c7a42cddc516a28eb09ff33 *tests/testthat/test-treeqza.R
f6aac83ea3079ae74cf66924d1704a77 *tests/testthat/test-utilities.R
39f1cc80ac4ad97deb86ec9cac26cde3 *vignettes/treeio.Rmd
