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TreeTools
View on CRAN: Click
here
Download and install TreeTools package within the R console
Install from CRAN:
install.packages("TreeTools")
Install from Github:
library("remotes")
install_github("cran/TreeTools")
Install by package version:
library("remotes")
install_version("TreeTools", "1.10.0")
Attach the package and use:
library("TreeTools")
Maintained by
Martin R. Smith
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-12-18
Latest Update: 2023-08-19
Description:
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
How to cite:
Martin R. Smith (2019). TreeTools: Create, Modify and Analyse Phylogenetic Trees. R package version 1.10.0, https://cran.r-project.org/web/packages/TreeTools
Previous versions and publish date:
0.1.2 (2019-12-18 16:00), 0.1.3 (2019-12-19 19:20), 0.1.4 (2020-03-04 17:30), 1.0.0 (2020-06-08 16:50), 1.1.0 (2020-07-07 11:10), 1.2.0 (2020-08-03 17:30), 1.3.0 (2020-09-22 18:00), 1.3.1 (2020-10-03 17:40), 1.4.0 (2020-10-19 20:50), 1.4.1 (2020-12-09 09:30), 1.4.2 (2021-01-26 19:20), 1.4.3 (2021-04-12 14:50), 1.4.4 (2021-04-20 12:00), 1.4.5 (2021-06-23 09:00), 1.5.0 (2021-09-08 10:00), 1.5.1 (2021-10-06 14:00), 1.6.0 (2022-01-12 15:22), 1.7.0 (2022-03-21 09:50), 1.7.1 (2022-03-25 15:10), 1.7.2 (2022-05-24 21:10), 1.7.3 (2022-07-20 16:30), 1.8.0 (2022-09-15 11:40), 1.9.0 (2022-11-28 21:00), 1.9.1 (2023-03-20 18:00), 1.9.2 (2023-04-27 11:42)
Other packages that cited TreeTools R package
View TreeTools citation profile
Other R packages that TreeTools depends,
imports, suggests or enhances
Functions, R codes and Examples using
the TreeTools R package
Some associated functions: AddTip . AncestorEdge . ApeTime . ArtificialExtinction . CharacterInformation . CladeSizes . CladisticInfo . ClusterTable-methods . ClusterTable . CollapseNode . CompatibleSplits . Consensus . ConsensusWithout . ConstrainedNJ . DescendantEdges . DoubleFactorial . DropTip . EdgeAncestry . EdgeDistances . EndSentence . EnforceOutgroup . ExtractTaxa . GenerateTree . Hamming . ImposeConstraint . KeptPaths . KeptVerts . LabelSplits . LeafLabelInterchange . ListAncestors . Lobo.data . MRCA . MSTEdges . MakeTreeBinary . MatrixToPhyDat . MorphoBankDecode . N1Spr . NDescendants . NJTree . NPartitionPairs . NRooted . NSplits . NTip . NewickTree . Neworder . NodeDepth . NodeOrder . NonDuplicateRoot . PairwiseDistances . PathLengths . PhyToString . PolarizeSplits . ReadCharacters . ReadTntTree . Renumber . RenumberTips . Reorder . RightmostCharacter . RoguePlot . RootNode . RootTree . SampleOne . SortTree . SpectrumLegend . SplitFrequency . SplitInformation . SplitMatchProbability . Splits . SplitsInBinaryTree . Stemwardness . Subsplit . Subtree . SupportColour . TipLabels . TipsInSplits . TotalCopheneticIndex . TreeIsRooted . TreeNumber . TreeShape . TreeTools-package . TreesMatchingSplit . TreesMatchingTree . TrivialSplits . TrivialTree . Unquote . UnrootedTreesMatchingSplit . UnshiftTree . WriteTntCharacters . as.Newick . as.multiPhylo . brewer . dot-RandomParent . doubleFactorials . edge_to_splits . logDoubleFactorials . match.Splits . nRootedShapes . print.TreeNumber . sapply64 . sort.multiPhylo . xor .
Some associated R codes: AddTip.R . ArtificialExtinction.R . BigInteger.R . ClusterTable.R . Combinatorics.R . Consensus.R . DropTip.R . ImposeConstraint.R . Information.R . KeptPaths.R . KeptVerts.R . PathLengths.R . RcppExports-manual.R . RcppExports.R . ReadTntTree.R . RoguePlot.R . SplitFunctions.R . Splits.R . Stemwardness.R . Support.R . TotalCopheneticIndex.R . TreeNumber.R . TreeTools-package.R . as.matrix.R . as.multiPhylo.R . data.R . helper_functions.R . mst.R . parse_files.R . phylo.R . sort.R . split_analysis.R . tree_comparison.R . tree_display.R . tree_generation.R . tree_information.R . tree_numbering.R . tree_properties.R . tree_rearrangement.R . tree_shape.R . tree_write.R . zzz.R . Full TreeTools package functions and examples
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