phangorn

Overview

About

Maintained by Klaus SchliepFirst published 2008-03-2570 releasesCRAN page ↗GitHub ↗

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).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phangorn", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("KlausVigo/phangorn")

Development version from KlausVigo/phangorn. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phangorn

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phangorn

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phangorn

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 13.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.02

8.3%

Coverage · measured lines

100%

Documentation · exports

14

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 223 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 93%
Return-value docs: 97%
References docs: 51%

Downloads

308.5K

CRAN downloads in the past year

Rank #740 · ~845/day · ~25.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

21.9K30 days

75.1K90 days

308.5K1 year

Compare downloads with other packages →

Also on1.7K r2u37 autocran29.3K conda_forge230 bioconda67 c2d4u

Repository

GitHub ↗ klausvigo/phangorn

215Stars

41Forks

29Open issues

0Open PRs

1Releases

2,943Commits

13Contributors

rphylogenetic-analysisphylogeneticsr-packagerstats

2,943 commits · Last activity 2026-07-06 · -0.5% stars, 30d

Stars over time

2025-07-04 · 2052026-07-10 · 215

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/klausvigo/phangorn on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0ape

Imports (13)

digest fastmatch genericsgraphicsgrDevicesigraph (>= 1.0)Matrixmethodsparallelquadprog Rcppstatsutils

LinkingTo (1)

Rcpp

Suggests (13)

apex Biostrings ggseqlogo ggplot2 knitr magick rgl rmarkdown seqinr testthat tinytest vdiffr xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

60direct

69indirect

and 12 more packages.

Code & Tests

Code Composition

R 20,146 (61%)Rd 5,614 (17%)C 2,853 (9%)C++ 1,788 (5%)Vignettes 1,398 (4%)Other 1,377 (4%)

Code characteristics

Object systems

S384

Cyclomatic complexity: 3.0 median / 110 max
Test cases: 329 / 0.02 per code line

Test coverage

Line coverage

8%

Expression

8.7%

Tests / Examples

8.3% / 57% ex

Functions

712 166 exported

Complexity

5.7 avg / 110 max

Call network

712 nodes / 990 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

712 functions

Function	Cyclo	Coverage
AICc exp	1	0%
Ancestors exp	8	0%
CI exp	2	0%
KF.dist exp	9	0%
NJ exp	1	0%
RF.dist exp	9	0%

People & History

People (18)

Maintainer (1)

Klaus Schliep

Author, Maintainer

Authors (5)

Klaus Schliep

Author, Maintainer

Iris Bardel-Kahr

Author · added in 2.11.1

Emmanuel Paradis

Author · added in 1.4-1

Alastair Potts

Author · added in 2.0.0

Leonardo de Oliveira Martins

Author · added in 2.1.1

Contributors (13)

Jeremy Beaulieu

Contributor · added in 2.6.2

Richel Bilderbeek

Contributor · added in 2.5.3

Joseph Brown

Contributor · added in 2.11.1

Santiago Claramunt

Contributor · added in 2.11.1

Mike Gilchrist

Contributor · added in 2.6.2

Keren Halabi

Contributor · added in 2.5.3

Michelle Kendall

Contributor · added in 2.0.4

Brian O'Meara

Contributor · added in 2.6.2

Show 5 more contributors

Long Qu

Contributor · added in 2.6.2

Liam Revell

Contributor · added in 2.6.2

Cyrill Stachniss

Contributor · added in 2.1.1

Tim W. White

Contributor · added in 2.1.1

Kristin Winchell

Contributor · added in 2.5.5

Listed in earlier versions (2)

Joseph

no longer listed · 2.12.1

Santiago

no longer listed · 2.12.1

Package Timeline

70 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
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R 4.5.0 released · 2025-04-11
2.12.1Latest
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.1.0 released · 2021-05-18
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R 2.8.0 released · 2008-10-20
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R 2.7.0 released · 2008-04-22
0.0-1
2008-03-25
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R 2.6.0 released · 2007-10-03

Package metadata

First published: 2008-03-25
Total releases: 70 / 18 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 192 KB / 4 files
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics