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phangorn

Phylogenetic Reconstruction and Analysis

v2.12.1 · Sep 17, 2024 · GPL (>= 2)
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Description

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

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CRAN Check Status

3 NOTE
11 OK
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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 NOTE
r-oldrel-macos-x86_64 NOTE
r-oldrel-windows-x86_64 NOTE
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (3 non-OK)
NOTE r-oldrel-macos-arm64

installed package size

installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   4.0Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.2Mb

Check History

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-oldrel-macos-arm64

installed package size

installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   4.0Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.2Mb

Reverse Dependencies (58)

depends

MSCquartets apex windex

imports

BSS BoSSA DCLEAR EnvNJ EvoPhylo LDM MonoPhy MorphSim OUwie POMS STraTUS SeqFeatR TML babette beastier bioregion coalescentMCMC corHMM dispRity dowser genBaRcode haplotypes hisse indelmiss ips markophylo microbial nodeSub orthGS paleotree pcmabc phyloregion phytools ppgm rapidphylo recluster rwty scistreer sketching taxize treespace

suggests

AntibodyForests CongreveLamsdell2016 MiscMetabar Quartet RRphylo RevGadgets TreeDist TreeSearch TreeTools ape immunarch mcbette tracerer treestructure

Dependency Network

Dependencies Reverse dependencies ape digest fastmatch generics igraph (>= 1.0) Matrix quadprog Rcpp MSCquartets apex windex BSS BoSSA DCLEAR EnvNJ EvoPhylo LDM MonoPhy MorphSim OUwie POMS STraTUS SeqFeatR +43 more reverse deps phangorn

Version History

new 2.12.1 Mar 10, 2026
updated 2.12.1 ← 2.11.1 diff Sep 16, 2024
updated 2.11.1 ← 2.10.0 diff Jan 22, 2023
updated 2.10.0 ← 2.9.0 diff Sep 17, 2022
updated 2.9.0 ← 2.8.1 diff Jun 15, 2022
updated 2.8.1 ← 2.8.0 diff Dec 14, 2021
updated 2.8.0 ← 2.7.1 diff Nov 8, 2021
updated 2.7.1 ← 2.7.0 diff Jul 12, 2021
updated 2.7.0 ← 2.6.3 diff May 2, 2021
updated 2.6.3 ← 2.6.2 diff Apr 5, 2021
updated 2.6.2 ← 2.5.5 diff Mar 21, 2021
updated 2.5.5 ← 2.5.3 diff Jun 18, 2019
updated 2.5.3 ← 2.4.0 diff Mar 22, 2019
updated 2.4.0 ← 2.3.1 diff Feb 15, 2018
updated 2.3.1 ← 2.2.0 diff Oct 31, 2017
updated 2.2.0 ← 2.1.1 diff Apr 2, 2017
updated 2.1.1 ← 2.0.4 diff Dec 3, 2016
updated 2.0.4 ← 2.0.3 diff Jun 20, 2016
updated 2.0.3 ← 2.0.2 diff Apr 30, 2016
updated 2.0.2 ← 2.0.1 diff Jan 22, 2016