c80db1433f084d9e282103f940a5744f *DESCRIPTION
36a2c087dcaafe90d95f77743b1a974d *NAMESPACE
0eaf88fab4de173e8efa4e20301430ff *NEWS.md
77aad145a8f63b9673f63a51bca6f0fc *R/ArtificialExtinction.R
d41d8cd98f00b204e9800998ecf8427e *R/BigInteger.R
458544dfe2c65aeb7ac65602956f71d7 *R/Combinatorics.R
01b2377ed4888e5a6f89d20703b20754 *R/Consensus.R
dfa7c9821f9af355a3a3ba298da57d1c *R/ImposeConstraint.R
51b6a08fb6cc4d98696ef35ba067e34d *R/Information.R
d41cde492ed89aebc399e1dfb49f6830 *R/RcppExports-manual.R
b2157fe0c512bab553cf3fc6c8de23f0 *R/RcppExports.R
cdded95c822f2ca65bc9a448e94a5503 *R/RoguePlot.R
0ee1d6d97ba0b7377cbc7ba56218736f *R/SplitFunctions.R
339ead2c6013596c938f7cc7385a38cc *R/Splits.R
bc316a2cc9257123ba0c5268262dda62 *R/Stemwardness.R
7f3e64e190430b547156f7e5f759f772 *R/Support.R
3afed1eecbfd88657d2d0a69e39bab72 *R/TotalCopheneticIndex.R
61eac7b79050727a81839c9c74bab177 *R/TreeNumber.R
346eccc17ab800137e89ea8183bddc3a *R/TreeTools-package.R
f7f490efe3911ace8ac55dee497b8b84 *R/as.multiPhylo.R
656a5c7860c12a4061cd95a2e4938a54 *R/data.R
1031c77d9f59dcfdc7632288061385c2 *R/helper_functions.R
a510cea36bc15a8d5638665dde52d91c *R/mst.R
13dbd489577a2f1ced2270d0d4a97a83 *R/parse_files.R
e1f0900f1dbccc23521c6de468f673f9 *R/phylo.R
a68f52d757f5980aaa5f059e639032f0 *R/split_analysis.R
9fb234ea6184e32a6cf0f17f6904af71 *R/sysdata.rda
6f6445247e67f18de43b7fff51f04256 *R/tree_comparison.R
50eb47278f0f8aa4f3d1f6c5cc7f805d *R/tree_display.R
dec047503547f7078fcb5636c2249722 *R/tree_generation.R
c0073eb9ca84fd554b0c6b80f64e0446 *R/tree_information.R
ddd6a717938f0cd5f768205e9575e9c5 *R/tree_numbering.R
66b9a14dd0e4575de2ab6c4af9631fb3 *R/tree_properties.R
a423ad67e8406161347b4463d1bdbcb7 *R/tree_rearrangement.R
c00f9507e1a2f284debda0f59f32f4a5 *R/tree_shape.R
366c385d88273fecb0f421e1afa36e30 *R/tree_write.R
98d562d1b274c5aa77175f3c8d0ff579 *R/zzz.R
bd1657a1449275bab33770e92cd8b348 *build/partial.rdb
1914fd98b17982e6cf1339d27d398e94 *build/vignette.rds
4f7f08498760060495a1138f1e456d8f *data/Lobo.RData
7a12bfe34746d63554ed9b3d31a0fb5c *data/brewer.R
bb0b8e0646742b8bbbe06122ab81a938 *data/nRootedShapes.R
88edcefaf797f0ede9a70efcd708ffd0 *data/nUnrootedShapes.R
806aadf10ac2e0ae477ffce74b720f72 *data/unrootedKeys.rda
da58fd7b83f0c90ef476e5f1bface8ba *inst/CITATION
ef7f9040edadcd55b4693e98ab46023e *inst/REFERENCES.bib
510f8b26471556b54714032821d4ca1a *inst/WORDLIST
2a33c016808841801938c7c7b2dcb1cb *inst/apa-old-doi-prefix.csl
7be48fe3f97d4e5c515b8fb4b62f5a9c *inst/doc/filesystem-navigation.Rmd
80411ea16bdd47257b9b36a8455cac72 *inst/doc/filesystem-navigation.html
bde6ddd47311d0879d826c28a5a2e6ac *inst/doc/load-data.R
63e9ffe9386a4925cd28e1e3bebe7c7d *inst/doc/load-data.Rmd
8d7ff023f73f6297dbb74897f556e661 *inst/doc/load-data.html
52c48e92a6ab50bff073cf47543193f9 *inst/doc/load-trees.R
8f6f9e95d1caba7f815f2cc56b27baf0 *inst/doc/load-trees.Rmd
106d74bef55faa2ba4ca535c7bd7409b *inst/doc/load-trees.html
38de4a03e1e8a5f07d46535ffc77277e *inst/extdata/input/dataset.nex
c11d9ad2158675f390443c6b64483931 *inst/extdata/input/notes.nex
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/otherfolder/empty.file
1a0bb364bcad07636e183bb94edd0b0d *inst/extdata/output/named.tre
390c2c6ce5db4839de4ec5aa9bc941e3 *inst/extdata/output/numbered.tre
307bd6e4eb9869f849fa0699a2c9b378 *inst/extdata/tests/ape-tree.nex
aa6feda919c49e2c7089b17745b7a3f3 *inst/extdata/tests/continuous.nex
a85e9f11ab78ea122572292d012ca2a7 *inst/extdata/tests/parse-nexus.nexus
1cd58a078d0dd8b5cd11da4bd3beee09 *inst/extdata/tests/tnt-dna.tnt
2871920befb8138b583a76dfa88ce4c5 *inst/extdata/tests/tnt-matrix.tnt
872071d2ef284e3869ea9cbbd10bc0cd *inst/extdata/tests/tnt-namedtree.tre
aadb9c227b26ca91b4390ae6755baa45 *inst/extdata/tests/tnt-tree.tre
5eaa5fdaf502d0b653055a84c06bdb9b *inst/extdata/tests/tnt-trees-and-matrix.tnt
f9006d7b84d026e4df0b6a959744cad1 *inst/include/TreeTools.h
7c733a1d5f518157fcf6dd95cc664e9f *inst/include/TreeTools/ClusterTable.h
5d9fea6e0da7405f94ba580ea8ba3f7a *inst/include/TreeTools/SplitList.h
9ec4c7960df7afc8071339d6591df378 *inst/include/TreeTools/renumber_tree.h
b82b5d2cb06ade73de429fc1665797c8 *inst/include/TreeTools/root_tree.h
ec9067074613bf7743e951f004943162 *inst/include/TreeTools/types.h
05a9210cc2756b752f3fba173aaeda59 *man/AddTip.Rd
828641731c09e3c200c134244a5c6acd *man/AncestorEdge.Rd
60713a49e08bab7af42d8fb5c6951979 *man/ApeTime.Rd
33ad2340c9365876cf37eaaebc11ba38 *man/ArtificialExtinction.Rd
1da3db32e1121a97f98715dbefdc57fa *man/CharacterInformation.Rd
1a7c3f7361becce0fb7b8f6d1d03ba76 *man/CladeSizes.Rd
87042ace7846fe8b7b53d3d335268979 *man/CladisticInfo.Rd
ad82a4b5f2198e963eaf8125363a9109 *man/CollapseNode.Rd
cbd99cb4fe96ab21d56cc03e7458eaf7 *man/CompatibleSplits.Rd
bf5f2966aba231987c6074d775fabb3b *man/Consensus.Rd
717c1510a8e502644246f4ffb7551c91 *man/ConsensusWithout.Rd
3b1aa0558fbdf8a5b9e10a8723977d99 *man/ConstrainedNJ.Rd
6dc5767b1686c60923e8b513a6584e12 *man/DescendantEdges.Rd
c88796f2953eec4597df9bc924c64157 *man/DoubleFactorial.Rd
7c1b1134f1e5cc5d50039b55333f1df8 *man/DropTip.Rd
1a6e7bf02226dbf3ec4e19ef96ca7cbe *man/EdgeAncestry.Rd
d760454d49d05a725fd082ff9f5ade93 *man/EdgeDistances.Rd
fbf94010b47d02ebc86a1f0cdd643555 *man/EndSentence.Rd
255eb6b1af6146a7df7fe5ee0c96955f *man/EnforceOutgroup.Rd
1dbe18d10cdd0e23e8be68b081fa31a5 *man/ExtractTaxa.Rd
0d3f9b97648c2d764eff12bab7f7d90f *man/GenerateTree.Rd
91ba963431730d4c4f1bc4cc8113fe83 *man/Hamming.Rd
101055661d72f365b0c1b3896edd2254 *man/ImposeConstraint.Rd
13c1e972a8afa25939bee58a8d393661 *man/LabelSplits.Rd
d76674859c3418db31ec9bb4af7caffe *man/LeafLabelInterchange.Rd
5c88df303110bec2ee450aa6000c7398 *man/ListAncestors.Rd
603528547b53bc9a041b6d82a105433e *man/Lobo.data.Rd
1e4a5e3ee6dd58c2335f09bab1ba5818 *man/MRCA.Rd
a2ab3c0dd17af1f9f62540a269f19d21 *man/MSTEdges.Rd
38f15f8621dad3d760a16e01c28b744d *man/MakeTreeBinary.Rd
c5d8375336b73bb7407dcc0a0166c2ae *man/MatrixToPhyDat.Rd
4ee602388a9586d1198869075c2d5763 *man/MorphoBankDecode.Rd
2298ce707bfa2304ed6356c1b096d6d9 *man/N1Spr.Rd
2acc324bf05e3add8076fae4909088ac *man/NDescendants.Rd
e07db055ea8a5ead8070bbd3f09d41a3 *man/NJTree.Rd
372b45899f393d5c5516954612ffc1ba *man/NPartitionPairs.Rd
ce7a96f457f44b2ffb26884e4dd8c148 *man/NRooted.Rd
d3bb806a98927f6b7510914fe4ab6717 *man/NSplits.Rd
78ed0c4862faf036876aa1ad520bda5a *man/NTip.Rd
6d8c77e944d714845608303fb092c20e *man/NewickTree.Rd
44643aa29310865a2ee85fd25c6e7a58 *man/Neworder.Rd
7df0de750c0f35d2e3d7102c82230ce1 *man/NodeDepth.Rd
18c6fa404c17955ccdb5e93e8a140c4d *man/NodeOrder.Rd
2a0d1376b8eb721f17bd0ab52f4c5668 *man/NonDuplicateRoot.Rd
08d590e67452cb70b808b2e1d18c9c0b *man/PairwiseDistances.Rd
b4928c2b8668e36cd346b5825dfa2393 *man/PhyToString.Rd
df3a99d0fb068bf09a9b3b462f59110d *man/PolarizeSplits.Rd
00bbef316481cc818a9a5145d4495bd6 *man/ReadCharacters.Rd
3d5698d824d374df11c435df6f68e845 *man/ReadTntTree.Rd
ea2f4bf2eff485857b975736ad35986d *man/Renumber.Rd
a7d4362acc70300dc830b65bf2e65465 *man/RenumberTips.Rd
36818df47cacff371c58b933718abaa5 *man/Reorder.Rd
f385ba797e695852a442acc806a0a128 *man/RightmostCharacter.Rd
882b48703dd778456ad5e7ada7ebb119 *man/RoguePlot.Rd
347125c970cf2336fbf5ac4badcc1f54 *man/RootNode.Rd
0b1abcf46d2d84bffb73ed11ddcc2143 *man/RootTree.Rd
e1bc7c2ffae1cac8395bd98c298bd27d *man/SampleOne.Rd
c3d84f05f185b4ce66937fc00343cf67 *man/SingleTaxonTree.Rd
c49156a82af1182b2a7630bb7581ca28 *man/SortTree.Rd
5461a78a04a7fd4d6070df54c7a251c5 *man/SplitFrequency.Rd
4ae95ecace6e62a1117da6d6c940689c *man/SplitInformation.Rd
000f139f98ffb33fdee64914a3b32d02 *man/SplitMatchProbability.Rd
ca3573a326780193d44850ce631ec0d1 *man/Splits.Rd
a3cde0a8619febb2a2f6938982eb0601 *man/SplitsInBinaryTree.Rd
dfacbfbf0cb4ca2121bbdba8d09881c2 *man/Stemwardness.Rd
9ff31af48800b197a2dc5511dba14a0f *man/Subsplit.Rd
357716a7c8b6f3fc9b63c1dc5e10b477 *man/Subtree.Rd
0f611a747488b25ad792d70a53bd2bf2 *man/SupportColour.Rd
e08fa597b88724cf38dadf44cc83507e *man/TipLabels.Rd
f4a0d002150a01cd24234996af79ee73 *man/TipsInSplits.Rd
dc92fb3fd9032d60dfdab805b5437032 *man/TotalCopheneticIndex.Rd
88965a2a8f87fd0116b26e40e3344f09 *man/TreeIsRooted.Rd
7548ef714054156ab68096bbefe8bad8 *man/TreeNumber.Rd
b933c966da69feb91db6114563b2ec35 *man/TreeShape.Rd
322171c0dfcac7b6944ca7b312e2ec70 *man/TreeTools-package.Rd
5137ca579278e231a2ed45570e3b08c7 *man/TreesMatchingSplit.Rd
24d2d6578a66a24a7a4dca7c31ecdb67 *man/TreesMatchingTree.Rd
153f6f39ab600cb8dd74c7bb118f0df2 *man/TrivialSplits.Rd
8a952e7b18a95e7f65f3edf5c17ebf77 *man/Unquote.Rd
e1d18bcde695fcfb659ba7a04dc6cc80 *man/UnrootedTreesMatchingSplit.Rd
98299ee97f231e0e4de870eaed52a000 *man/UnshiftTree.Rd
20723ac949d5897e699b7aed720ef17c *man/WriteTntCharacters.Rd
eee6b0d9e36889d3d84abadf8e909936 *man/as.Newick.Rd
375b024a734aaeb8d828d8976a78eaa1 *man/as.multiPhylo.Rd
d984df86ae2dd417fb3f03a6eff299d0 *man/brewer.Rd
5beba98d754aaf0d27b0fb29b2233e3e *man/dot-RandomParent.Rd
c862dedc16085134d115c7693ef26919 *man/doubleFactorials.Rd
b43388c69a1d40377c7169ea9100f637 *man/figures/Stemwardness.png
cb1e46f469cfbbbde29c8b5113e1d789 *man/figures/lifecycle-archived.svg
c0d2e5a54f1fa4ff02bf9533079dd1f7 *man/figures/lifecycle-defunct.svg
a1b8c987c676c16af790f563f96cbb1f *man/figures/lifecycle-deprecated.svg
c3978703d8f40f2679795335715e98f4 *man/figures/lifecycle-experimental.svg
952b59dc07b171b97d5d982924244f61 *man/figures/lifecycle-maturing.svg
27b879bf3677ea76e3991d56ab324081 *man/figures/lifecycle-questioning.svg
53b3f893324260b737b3c46ed2a0e643 *man/figures/lifecycle-stable.svg
1c1fe7a759b86dc6dbcbe7797ab8246c *man/figures/lifecycle-superseded.svg
1ada11d02c8c52742fb05690800b694d *man/logDoubleFactorials.Rd
d46fa01d31dfb69d1bd3c3c56283cb77 *man/match.Rd
9a4a4181863dc9ab66fa67c54a86d055 *man/nRootedShapes.Rd
5c1affb3cddf3b83333a15298093058c *man/print.TreeNumber.Rd
60af5972f0bf6b138f7f94a266851b37 *man/sapply64.Rd
50975b0b8e645c4e7b535860ba4faa5c *src/RcppExports-manual.cpp
9aa487c6fffb20db0a523e85599585fd *src/RcppExports.cpp
a46c43b5eff7aef6f0983256da6c028a *src/TreeTools-init.c
fc222debdfb2750e4802a2dbac85e38c *src/ape_reorder.h
aade4452cb88a19c0f55905f1699c2a9 *src/as_newick.cpp
15c0fdec71391168a7d81f13341bf77f *src/consensus.cpp
1b6a6b6c8b546bcff687667d91bb1782 *src/drop_tip.cpp
6a253cf2d635feb8759c9ef5b3bdc772 *src/int_to_tree.cpp
24ea0617b469b8b4839bb216667d64be *src/minimum_spanning_tree.cpp
3394842b25daad08409984e7509275fb *src/splits.cpp
ade98fbd9ef533a123ff02881aed5653 *src/splits_to_tree.cpp
c4e9e2b7da5ea46ba0e1d321f8e664f5 *src/tips_in_splits.cpp
a76dca9d57cf230cfc60d9fc9e6e4adb *src/tree_shape.cpp
84072f97e1b51491b621f7fd68582d30 *tests/benchmark/benchmark-consensus.R
5997537fb6f5ac3dbd842a6621a0ed60 *tests/benchmark/benchmark-preorder.R
dddd680474aa4bb6ced59539a358d904 *tests/figs/rogueplot.svg
2e634fb9fd55644284814fcd3f3971db *tests/spelling.R
a418111bda7a5b89800afa5d3c6da2d8 *tests/testthat.R
3bc91a5ed6f488fc15ddb01ce7233dfa *tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg
913ceb3883760430d25406496e20a583 *tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg
69f72fbebb042ed59f3be0497a56d6fd *tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg
daede718a12a50289d4eb2fb6ce72b90 *tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg
e0c54c52a7f26c7febdb1291f5c1d7e6 *tests/testthat/_snaps/Support/labelsplits-names.svg
23a11c9d4b741b10fea3a0580dfbaeb0 *tests/testthat/_snaps/Support/labelsplits.svg
96fe8be9631fd5202772c113bd3daa9e *tests/testthat/_snaps/mst/mst-plotting.svg
597fe201961b312fe0e2593a9b6a9288 *tests/testthat/test-ArtificialExtinction.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-BigInteger.R
2e2147db11f61fa4a17cabf9271ea37f *tests/testthat/test-ImposeConstraint.R
85edb1460b9e95214b1469ead4e7d437 *tests/testthat/test-RoguePlot.R
3ae0fdc4d5431d0219dde485c4f2511f *tests/testthat/test-SplitFunctions.R
518f5ceccc9b7705de09d92020033b55 *tests/testthat/test-Splits.R
b41540eae76d777943601d7e3dd9ec2c *tests/testthat/test-Stemwardness.R
03e15bcdb5a9705c858bf416755b7731 *tests/testthat/test-Support.R
f66c170358da7fe275d2fa5677e784a3 *tests/testthat/test-TotalCopheneticIndex.R
9f74b5d9ab1aaf0681933078b59d9032 *tests/testthat/test-TreeNumber.R
939ec1e345b6cbdeace954f43040b543 *tests/testthat/test-as.multiPhylo.R
b1e223c1355cb30396356b31a72964d0 *tests/testthat/test-combinatorics.R
34eab993c09d16e11b4cda55192d9f65 *tests/testthat/test-consensus.R
f4e5ec92c520218f05489273dead36ab *tests/testthat/test-drop_tip.cpp.R
c292d0b477c67739a511c0ba81631a35 *tests/testthat/test-helper_functions.R
2f7e9bc483f087726aff7c26f29e4907 *tests/testthat/test-information.R
f95f2c62c400815573f1da4417cda27c *tests/testthat/test-int_to_tree.cpp.R
05c42c10bfbffdc2b560835e343b670e *tests/testthat/test-mst.R
73dc1e651f0393f8b5ea9535d9ce9511 *tests/testthat/test-parsers.R
d3aff3e5dfecf480bba7d679d88dfa29 *tests/testthat/test-phylo.R
f811debe7b51151c55ecbaf79ae31e67 *tests/testthat/test-root_tree.h.R
e1824b6069497e5dbdf4e58c93facc52 *tests/testthat/test-split_analysis.R
ac15cc794adbbd588fb43c222a49ed59 *tests/testthat/test-splits.cpp.R
e845fafb566b374a42c950d70c0ae055 *tests/testthat/test-tree_comparison.R
880b138caed401e3cf4322756b412e7f *tests/testthat/test-tree_display.R
69914dc84ecea34a29b77d5e753e0508 *tests/testthat/test-tree_generation-random.R
f5465e7c3987699f3189ba5618be3bf2 *tests/testthat/test-tree_generation.R
baae5ddd8cbf96cd9d07b2ca892ef6cf *tests/testthat/test-tree_information.R
6c113672884942986101440152fa8501 *tests/testthat/test-tree_numbering.R
c939133b33cad3060e447e6d355896d7 *tests/testthat/test-tree_properties.R
8a840e3c09cb0fc864268624c9cda32c *tests/testthat/test-tree_rearrange.R
5b02f86ef41ba71e5dc8fba1cf0f0a95 *tests/testthat/test-tree_shape.R
733e44faf903d66b5e7ba7bebab9b52f *tests/testthat/test-tree_write.R
7be48fe3f97d4e5c515b8fb4b62f5a9c *vignettes/filesystem-navigation.Rmd
63e9ffe9386a4925cd28e1e3bebe7c7d *vignettes/load-data.Rmd
8f6f9e95d1caba7f815f2cc56b27baf0 *vignettes/load-trees.Rmd
