ape
5.8-1Analyses of Phylogenetics and Evolution
395packages depend
1.5Mdownloads / year
–test coverage
13/13checks pass
Overview
About
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Install
Health
CRAN checks
13OK
Slowest check: 8.0 min · r-devel-windows-x86_64
Code health
None
Tests · ratio 0.00
not tracked
Coverage
100%
Documentation · exports
9
Dependencies · direct
Check history
- OK2026-08-0513 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- NOTE2026-08-0112 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- OK2026-04-2512 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- NOTE2026-04-2212 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-04-1811 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
Show 1 earlier snapshots
- NOTE2026-03-1012 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
Documentation
Documentation
READMEYes · 15 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo
- Examples that run
- 93%
- Documented parameters
- 94%
- Return-value docs
- 91%
- References docs
- 51%
Downloads
1.5M
CRAN downloads in the past year
Rank #306 · ~4K/day · ~122K/mo
Daily download trend is not available in this view yet.
110.7K30 days
377.9K90 days
1.5M1 year
Also on12.4K r2u113 autocran491.7K conda_forge282 c2d4u
Repository
Repository
74Stars
12Forks
7Open issues
0Open PRs
0Releases
282Commits
12Contributors
License GPL-2.0 · 282 commits · Last activity 2026-06-17 · 0% stars, 30d
Stars over time
2025-06-16 · 692026-07-07 · 74
Forks over time
2025-02-04 · 112026-07-07 · 12
Issues over time
2025-07-30 · 72026-07-07 · 7
PRs over time
2025-03-23 · 02026-07-07 · 0
Repository practices
Upstream repositoryBeta
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/emmanuelparadis/ape on 2026-08-09.
Continuous integration (1)
GitHub Actions
Dependencies
Declared dependencies
8 external dependencies (excludes base and recommended)
Depends (1)
R >= 3.2.0
LinkingTo (1)
Enhances (0)
none
Reverse dependencies
395direct
130indirect
AnacondaBAMMtoolsBarcodingRCladdisFDJNplotsMCMCglmmMPSEMMSCquartetsMSCsimtesterMonoPhyOUwiePhylogeneticEMRNeXMLRphyloparsTreeSimTreeToolsVDJgermlinesapexaphylobayoucapercaticauphyclootlcoalescentMCMCconvevolcorHMMdispRitydistorydiversitreegeigerhisseipsjrichmegatreesmotmotmvMORPHnichevolnodeSubpaleoDivpaleotreepegasperspectevpezphangornphyclustphyloTop
and 347 more packages.
Code & Tests
Datasets
People & History
People (33)
Maintainer (1)
Author, Maintainer, Copyright holder · added in 1.2-7
Authors (33)
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Copyright holders (33)
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Listed in earlier versions (9)
no longer listed · 1.2-4 to 1.2-5
no longer listed · 1.2-7 to 2.5-1
Package Timeline
104 releases. Pick two to compare their code metrics. R releases are shown for context.
- RR 4.6.0 released · 2026-04-24
- RR 4.5.0 released · 2025-04-11
- 5.8-1Latest
- RR 4.4.0 released · 2024-04-24
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- RR 4.3.0 released · 2023-04-21
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- RR 4.2.0 released · 2022-04-22
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- 5.6-12022-01-07 · diff ↗
- 5.62021-12-21 · diff ↗
- RR 4.1.0 released · 2021-05-18
- 5.52021-04-25 · diff ↗
- 5.4-12020-08-13 · diff ↗
- 5.42020-06-03 · diff ↗
Show 123 earlier events
- RR 4.0.0 released · 2020-04-24
- RR 3.6.0 released · 2019-04-26
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- 5.22018-09-24 · diff ↗
- RR 3.5.0 released · 2018-04-23
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- 5.02017-10-30 · diff ↗
- RR 3.4.0 released · 2017-04-21
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- 3.52016-05-24 · diff ↗
- RR 3.3.0 released · 2016-05-03
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- RR 3.2.0 released · 2015-04-16
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- RR 3.1.0 released · 2014-04-10
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- RR 3.0.0 released · 2013-04-03
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- RR 2.15.0 released · 2012-03-30
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- RR 2.14.0 released · 2011-10-31
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- RR 2.13.0 released · 2011-04-13
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- RR 2.12.0 released · 2010-10-15
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- RR 2.11.0 released · 2010-04-22
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- RR 2.10.0 released · 2009-10-26
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- RR 2.9.0 released · 2009-04-17
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- RR 2.8.0 released · 2008-10-20
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- RR 2.7.0 released · 2008-04-22
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- RR 2.6.0 released · 2007-10-03
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- RR 2.5.0 released · 2007-04-24
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- RR 2.4.0 released · 2006-10-03
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- RR 2.3.0 released · 2006-04-24
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- RR 2.2.0 released · 2005-10-06
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- RR 2.0.0 released · 2004-10-04
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- RR 1.9.0 released · 2004-04-12
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- RR 1.8.0 released · 2003-10-08
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- RR 1.6.0 released · 2002-10-01
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- RR 1.5.0 released · 2002-04-29
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Package metadata
- First published
- 2002-08-31
- Total releases
- 104 / 24 yrs
- License
- GPL-2 | GPL-3 OSI
- Minimum R
- ≥ 3.2.0
- Bundled data
- 125 KB / 16 files
- Download size
- 1.4 MB
- Installed size
- not tracked yet
- With dependencies
- not tracked yet
Appears in task views
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Run in R for the authors' preferred citation:
citation("ape")Paradis, E., Blomberg, S., Bolker, B., Brown, J., Claramunt, S., Claude, J., Cuong, H. S., Desper, R., Didier, G., Durand, B., Dutheil, J., Ewing, R., Gascuel, O., Guillerme, T., Heibl, C., Ives, A., Jones, B., Krah, F., Lawson, D., Lefort, V., Legendre, P., Lemon, J., Louvel, G., Marcon, E., Marotta, F., McCloskey, R., Nylander, J., Opgen-Rhein, R., Popescu, A., Royer-Carenzi, M., Schliep, K., Strimmer, K., & de Vienne, D. (2024). ape: Analyses of Phylogenetics and Evolution (Version 5.8-1) [Computer software]. https://doi.org/10.32614/CRAN.package.ape
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