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phangorn
Phylogenetic Reconstruction and Analysis
View on CRAN: Click
here
Download and install phangorn package within the R console
Install from CRAN:
install.packages("phangorn")
Install from Github:
library("remotes")
install_github("cran/phangorn") Install by package version:
library("remotes")
install_version("phangorn", "2.12.1") Attach the package and use:
library("phangorn")
Maintained by
Klaus Schliep
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2008-03-25
Latest Update: 2024-09-17
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).
How to cite:
Klaus Schliep (2008). phangorn: Phylogenetic Reconstruction and Analysis. R package version 2.12.1, https://cran.r-project.org/web/packages/phangorn. Accessed 07 Mar. 2026.
Previous versions and publish date:
0.0-1 (2008-03-25 10:05), 0.0-2 (2008-07-20 18:08), 0.0-3 (2008-10-28 13:58), 0.0-4 (2008-12-22 09:06), 0.0-5 (2009-01-22 09:36), 0.99-2 (2009-07-21 14:29), 0.99-3 (2009-10-30 18:32), 0.99-4 (2009-11-27 19:19), 0.99-5 (2010-01-15 20:57), 0.99-6 (2010-01-27 12:10), 1.0-0 (2010-03-18 20:16), 1.0-1 (2010-04-15 16:57), 1.0-2 (2010-05-16 18:20), 1.1-0 (2010-08-28 08:20), 1.1-1 (2010-09-03 21:38), 1.1-2 (2010-09-21 10:15), 1.2-0 (2010-11-22 12:10), 1.3-0 (2011-01-31 19:51), 1.3-1 (2011-02-14 20:44), 1.4-0 (2011-03-27 17:55), 1.4-1 (2011-06-30 19:03), 1.5-0 (2011-12-10 12:13), 1.5-1 (2011-12-13 09:36), 1.6-0 (2012-04-05 22:43), 1.6-3 (2012-07-01 11:28), 1.6-4 (2012-08-02 14:22), 1.6-5 (2012-10-10 12:50), 1.7-1 (2012-10-30 18:20), 1.7-4 (2013-04-04 15:43), 1.99-1 (2013-08-21 20:01), 1.99-5 (2014-01-02 19:18), 1.99-7 (2014-02-02 14:21), 1.99-8 (2014-10-07 08:55), 1.99-9 (2014-10-09 23:47), 1.99-11 (2014-11-11 09:04), 1.99-12 (2015-02-14 00:46), 1.99-13 (2015-04-08 00:44), 1.99.14 (2015-07-09 18:11), 2.0.0 (2015-12-10 23:03), 2.0.1 (2015-12-15 00:59), 2.0.2 (2016-01-23 00:39), 2.0.3 (2016-05-01 00:42), 2.0.4 (2016-06-21 08:32), 2.1.1 (2016-12-04 11:42), 2.2.0 (2017-04-03 22:40), 2.3.1 (2017-11-01 17:38), 2.4.0 (2018-02-16 00:15), 2.5.3 (2019-03-23 23:30), 2.5.5 (2019-06-19 06:40), 2.6.2 (2021-03-22 15:20), 2.6.3 (2021-04-06 14:10), 2.7.0 (2021-05-03 18:20), 2.7.1 (2021-07-13 18:00), 2.8.0 (2021-11-09 11:20), 2.8.1 (2021-12-15 01:20), 2.9.0 (2022-06-16 17:10), 2.10.0 (2022-09-18 10:26), 2.11.1 (2023-01-23 11:10)
Other packages that cited phangorn R package
View phangorn citation profile
Other R packages that phangorn depends,
imports, suggests or enhances
Complete documentation for phangorn
Functions, R codes and Examples using
the phangorn R package
Some associated functions: Ancestors . CI . Laurasiatherian . NJ . SH.test . SOWH.test . add.tips . addConfidences . add_ci . add_edge_length . allTrees . ancestral.pml . as.networx . as.phyDat . as.splits . bab . baseFreq . bootstrap.pml . chloroplast . cladePar . coalSpeciesTree . codonTest . consensusNet . cophenetic.networx . delta.score . densiTree . designTree . dfactorial . discrete.gamma . dist.hamming . dist.p . distanceHadamard . dna2codon . getClans . hadamard . identify.networx . image.phyDat . lento . mast . maxCladeCred . midpoint . mites . modelTest . neighborNet . nni . parsimony . phangorn-internal . phangorn-package . phyDat . plot.networx . plotBS . pml.control . pml.fit . pml . pmlCluster . pmlMix . pmlPart . pml_bb . read.aa . read.nexus.splits . read.phyDat . reexports . simSeq . splitsNetwork . superTree . transferBootstrap . treedist . upgma . writeDist . yeast .
Some associated R codes: Coalescent.R . Densi.R . F3X4.R . RcppExports.R . SH.R . SOWH.R . addConfidences.R . ancestral_pml.R . bab.R . baseFreq.R . bipart.R . bootstrap.R . candidate_tree.R . cladePar.R . clanistic.R . codon.R . codonTest.R . delta.score.R . discrete.gamma.R . dist.p.R . distSeq.R . distTree.R . draw_CI.R . fitch64.R . hadamard.R . hash_phylo.R . image_phyDat.R . lento.R . mast.R . maxCladeCred.R . modelTest.R . neighborNet.R . networx.R . parsimony.R . phangorn-package.R . phyDat.R . phyDat2.R . phyDat_conversion.R . phylo.R . pmlMix.R . pmlPart.R . pmlPen.R . pml_bb.R . pml_control.R . pml_generics.R . read.nexus.splits.R . read.phyDat.R . sankoff.R . simSeq.R . splits.R . splitsNetwork.R . superTree.R . transferBootstrap.R . treeManipulation.R . treeRearrangement.R . treedist.R . zzz.R . Full phangorn package functions and examples
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