TreeTools
Create, Modify and Analyse Phylogenetic Trees
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, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; 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.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | WARNING |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | WARNING |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (15 non-OK)
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Rd files
2026-02-12 17:41:55.912 R[9470:188955] XType: Using static font registry.
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 4.8Mb
installed package size
installed size is 6.8Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 4.5Mb
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Rd files
2026-02-12 17:57:07.339 R[32376:687541] XType: Using static font registry.
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Check History
WARNING 11 OK · 1 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
Rd files
2026-02-12 17:57:07.339 R[32376:687541] XType: Using static font registry.
installed package size
installed size is 6.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 4.8Mb
installed package size
installed size is 6.8Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 4.5Mb