Other packages > Find by keyword >

TreeTools  

Create, Modify and Analyse Phylogenetic Trees
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", "2.0.0")



Attach the package and use:
library("TreeTools")
Maintained by
Martin R. Smith
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-12-18
Latest Update: 2025-07-21
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 2.0.0, https://cran.r-project.org/web/packages/TreeTools. Accessed 08 Jun. 2026.
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), 1.10.0 (2023-08-19 02:22), 1.11.0 (2024-06-05 18:50), 1.11.1 (2024-06-07 17:30), 1.12.0 (2024-07-25 15:40), 1.13.0 (2025-01-10 19:20), 1.13.1 (2025-04-07 15:10), 1.14.0 (2025-05-13 20:50), 1.15.0 (2025-07-21 16:20), 1.16.0 (2025-08-22 15:10), 1.16.1 (2025-08-25 01:50), 2.0.0 (2025-09-23 12:30), 2.1.0 (2026-02-11 11:20), 2.2.0 (2026-03-20 07:11), 2.3.0 (2026-04-23 12:10)
Other packages that cited TreeTools R package
View TreeTools citation profile
Other R packages that TreeTools depends, imports, suggests or enhances
Complete documentation for TreeTools
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

ODMeans  
OD-Means: k-Means for Origin-Destination
OD-means is a hierarchical adaptive k-means algorithm based on origin-destination pairs. In the fir ...
Download / Learn more Package Citations See dependency  
penppml  
Penalized Poisson Pseudo Maximum Likelihood Regression
A set of tools that enables efficient estimation of penalized Poisson Pseudo Maximum Likelihood reg ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
geofacet  
'ggplot2' Faceting Utilities for Geographical Data
Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequen ...
Download / Learn more Package Citations See dependency  
FluMoDL  
Influenza-Attributable Mortality with Distributed-Lag Models
Functions to estimate the mortality attributable to influenza and temperature, using distributed-la ...
Download / Learn more Package Citations See dependency  
AdvBinomApps  
Upper Clopper-Pearson Confidence Limits for Burn-in Studies under Additional Available Information
Functions to compute upper Clopper-Pearson confidence limits of early life failure probabilities and ...
Download / Learn more Package Citations See dependency  

27,372

R Packages

233,548

Dependencies

72,820

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA