f07b70d1f301f19c66c74b8fe7b9df62 *DESCRIPTION
6cf15f93bdea0c7e4cf97265364baa0a *NAMESPACE
fd83543c41aa083ee2ae99326330f2aa *NEWS.md
77aad145a8f63b9673f63a51bca6f0fc *R/ArtificialExtinction.R
d41d8cd98f00b204e9800998ecf8427e *R/BigInteger.R
458544dfe2c65aeb7ac65602956f71d7 *R/Combinatorics.R
8f1f854b2ca80df3ff5baa165c33d76a *R/Consensus.R
7f7f994712dc2373212d6d41dd8d3ecc *R/ImposeConstraint.R
6846eccee87a1839081b050207633d79 *R/Information.R
d41cde492ed89aebc399e1dfb49f6830 *R/RcppExports-manual.R
b2157fe0c512bab553cf3fc6c8de23f0 *R/RcppExports.R
0ee1d6d97ba0b7377cbc7ba56218736f *R/SplitFunctions.R
339ead2c6013596c938f7cc7385a38cc *R/Splits.R
bc316a2cc9257123ba0c5268262dda62 *R/Stemwardness.R
dd9eaf8817fa6d6a5fa0a5b525d28fc3 *R/Support.R
3afed1eecbfd88657d2d0a69e39bab72 *R/TotalCopheneticIndex.R
61eac7b79050727a81839c9c74bab177 *R/TreeNumber.R
346eccc17ab800137e89ea8183bddc3a *R/TreeTools-package.R
935d254d48c20863122f582f00c7647a *R/as.multiPhylo.R
656a5c7860c12a4061cd95a2e4938a54 *R/data.R
1031c77d9f59dcfdc7632288061385c2 *R/helper_functions.R
a510cea36bc15a8d5638665dde52d91c *R/mst.R
ad6308ee5c0b71866ae5254533c4a025 *R/parse_files.R
e1f0900f1dbccc23521c6de468f673f9 *R/phylo.R
a68f52d757f5980aaa5f059e639032f0 *R/split_analysis.R
9fb234ea6184e32a6cf0f17f6904af71 *R/sysdata.rda
6f6445247e67f18de43b7fff51f04256 *R/tree_comparison.R
b22e6ce59a377be70e989be64c5560a9 *R/tree_display.R
29910b4ec0a33538bca1e71039ed70a4 *R/tree_generation.R
c0073eb9ca84fd554b0c6b80f64e0446 *R/tree_information.R
edcdd785ba806484d4ba3b3ce0451159 *R/tree_numbering.R
bf5759a40fa69e2e5008aaa32dd43625 *R/tree_properties.R
e549748aa23a21e1bd776f9e6b505dc6 *R/tree_rearrangement.R
3b4e8516a06f81f7560a2c3071ca2ff3 *R/tree_shape.R
366c385d88273fecb0f421e1afa36e30 *R/tree_write.R
0afa46dbdaed16d6fd69602ca5fddb60 *R/zzz.R
0d0b66150158a807213d7864ac477d53 *build/partial.rdb
e1f76f9323e17b3ed2bf11d56eadef9a *build/vignette.rds
4f7f08498760060495a1138f1e456d8f *data/Lobo.RData
7a12bfe34746d63554ed9b3d31a0fb5c *data/brewer.R
bb0b8e0646742b8bbbe06122ab81a938 *data/nRootedShapes.R
88edcefaf797f0ede9a70efcd708ffd0 *data/nUnrootedShapes.R
806aadf10ac2e0ae477ffce74b720f72 *data/unrootedKeys.rda
e5cdd8259143f8a1b65612d379228f7f *inst/CITATION
2b61c177f5908908e8cc4912117d6b78 *inst/REFERENCES.bib
bda72fdb22451b96764419c5c1538207 *inst/WORDLIST
2a33c016808841801938c7c7b2dcb1cb *inst/apa-old-doi-prefix.csl
b22cb54396724ca5f839c64f143eb2b5 *inst/doc/filesystem-navigation.Rmd
2fcbb88144d051af7301928f60cd0007 *inst/doc/filesystem-navigation.html
9a31150877be73d927f433414f71373e *inst/doc/load-data.R
06ea1f0cf958fe4cae88f2abca2a9cb2 *inst/doc/load-data.Rmd
9e790a9cde4192121dea370fd60964e2 *inst/doc/load-data.html
52c48e92a6ab50bff073cf47543193f9 *inst/doc/load-trees.R
dc1f6d868417773541a01e184a8304c5 *inst/doc/load-trees.Rmd
6d9edde4cca1bc46f886ece488b486de *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
fee10072fa11771043674bbec951fcd2 *man/CharacterInformation.Rd
1a7c3f7361becce0fb7b8f6d1d03ba76 *man/CladeSizes.Rd
87042ace7846fe8b7b53d3d335268979 *man/CladisticInfo.Rd
ad82a4b5f2198e963eaf8125363a9109 *man/CollapseNode.Rd
607a294c1cf05d068edb9f5a631ec430 *man/CompatibleSplits.Rd
4e2a865d8dd47b9b5fed7241130e49ab *man/Consensus.Rd
7b008e8633ee821b7a87ae68a192bf5e *man/ConsensusWithout.Rd
2e3e20520d0c1b20a9c454b33f479fbc *man/ConstrainedNJ.Rd
6dc5767b1686c60923e8b513a6584e12 *man/DescendantEdges.Rd
c88796f2953eec4597df9bc924c64157 *man/DoubleFactorial.Rd
2b55e6740131a78ed1e932ddc98e3389 *man/DropTip.Rd
1a6e7bf02226dbf3ec4e19ef96ca7cbe *man/EdgeAncestry.Rd
d760454d49d05a725fd082ff9f5ade93 *man/EdgeDistances.Rd
fbf94010b47d02ebc86a1f0cdd643555 *man/EndSentence.Rd
255eb6b1af6146a7df7fe5ee0c96955f *man/EnforceOutgroup.Rd
1dbe18d10cdd0e23e8be68b081fa31a5 *man/ExtractTaxa.Rd
194b6c5dd84a04c6cb7ddc4b6d6891f7 *man/GenerateTree.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
c7fb750ae0134a94d22a894900a40bfd *man/MatrixToPhyDat.Rd
4ee602388a9586d1198869075c2d5763 *man/MorphoBankDecode.Rd
2298ce707bfa2304ed6356c1b096d6d9 *man/N1Spr.Rd
2acc324bf05e3add8076fae4909088ac *man/NDescendants.Rd
466307487a5c760935def0baa435f4a2 *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
4f250f994cf44c436e249541c040f3cb *man/PhyToString.Rd
df3a99d0fb068bf09a9b3b462f59110d *man/PolarizeSplits.Rd
bfbda5b54aa8b910e51bd813a4e6698e *man/ReadCharacters.Rd
3d5698d824d374df11c435df6f68e845 *man/ReadTntTree.Rd
ea2f4bf2eff485857b975736ad35986d *man/Renumber.Rd
a7d4362acc70300dc830b65bf2e65465 *man/RenumberTips.Rd
38a126984b3f09fcaeca7ede2eee006c *man/Reorder.Rd
f385ba797e695852a442acc806a0a128 *man/RightmostCharacter.Rd
3b85119466c2b3bade6d20c253326869 *man/RootNode.Rd
0b1abcf46d2d84bffb73ed11ddcc2143 *man/RootTree.Rd
e1bc7c2ffae1cac8395bd98c298bd27d *man/SampleOne.Rd
c3d84f05f185b4ce66937fc00343cf67 *man/SingleTaxonTree.Rd
c49156a82af1182b2a7630bb7581ca28 *man/SortTree.Rd
5461a78a04a7fd4d6070df54c7a251c5 *man/SplitFrequency.Rd
0495f6d93d3af56000f1cc2c51543f74 *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
cfa5c6312d25abec24370b46a63bfe23 *man/figures/Stemwardness.png
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
81009ab06150f8c7d5f04df4fef128f8 *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
a418111bda7a5b89800afa5d3c6da2d8 *tests/testthat.R
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
97a15f5de98a557ca8bf21ffb07fb6e7 *tests/testthat/test-ImposeConstraint.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
cd17e274a1d20ac058f287655ee834a8 *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
280a987567fbaa58f968fcc9e852db27 *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
89af2a2022b84c510238f889212e2e12 *tests/testthat/test-tree_comparison.R
880b138caed401e3cf4322756b412e7f *tests/testthat/test-tree_display.R
69914dc84ecea34a29b77d5e753e0508 *tests/testthat/test-tree_generation-random.R
17992d80e796ffffcebace471787c4d5 *tests/testthat/test-tree_generation.R
baae5ddd8cbf96cd9d07b2ca892ef6cf *tests/testthat/test-tree_information.R
93b02099b17d8cbc18d9b7b0e58f6307 *tests/testthat/test-tree_numbering.R
c939133b33cad3060e447e6d355896d7 *tests/testthat/test-tree_properties.R
3d80ea2b7c2da181392a69b554889e4f *tests/testthat/test-tree_rearrange.R
5b02f86ef41ba71e5dc8fba1cf0f0a95 *tests/testthat/test-tree_shape.R
733e44faf903d66b5e7ba7bebab9b52f *tests/testthat/test-tree_write.R
b22cb54396724ca5f839c64f143eb2b5 *vignettes/filesystem-navigation.Rmd
06ea1f0cf958fe4cae88f2abca2a9cb2 *vignettes/load-data.Rmd
dc1f6d868417773541a01e184a8304c5 *vignettes/load-trees.Rmd
