Package: phangorn 2.12.1.1

phangorn: Phylogenetic Reconstruction and Analysis

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).

Authors:Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Leonardo de Oliveira Martins [aut], Alastair Potts [aut], Iris Bardel-Kahr [aut], Tim W. White [ctb], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb], Joseph Brown [ctb], Santiago Claramunt [ctb]

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phangorn/json (API)
NEWS

# Install 'phangorn' in R:
install.packages('phangorn', repos = c('https://klausvigo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/klausvigo/phangorn/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

softwaretechnologyqualitycontrolphylogenetic-analysisphylogenetics

172 exports 203 stars 16.61 score 17 dependencies 136 dependents 192 mentions 2.2k scripts 22.5k downloads

Last updated 2 days agofrom:6e7fa24a17. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 12 2024
R-4.5-win-x86_64NOTEOct 12 2024
R-4.5-linux-x86_64NOTEOct 12 2024
R-4.4-win-x86_64NOTEOct 12 2024
R-4.4-mac-x86_64NOTEOct 12 2024
R-4.4-mac-aarch64NOTEOct 12 2024
R-4.3-win-x86_64NOTEOct 12 2024
R-4.3-mac-x86_64NOTEOct 12 2024
R-4.3-mac-aarch64NOTEOct 12 2024

Exports:acctranacgt2ryadd_boxplotadd_ciadd_edge_lengthadd_mutationsadd_supportadd.tipsaddConfidencesaddTrivialSplitsAICcallCircularSplitsallCompatallDescendantsallSitePatternallSplitsallTreesanc_parsanc_pmlAncestorsancestral.parsancestral.pmlas.ancestralas.Matrixas.MultipleAlignmentas.networxas.phyDatas.pmlas.splitsas.StringSetbabbaseFreqbootstrap.phyDatbootstrap.pmlc.phyDatcandidate_treecbind.phyDatChildrenCIcladeParcoalSpeciesTreecodon2dnacodonTestcompatiblecomposition_testconsensusNetcoordscreateLabeldelta.scoredensiTreeDescendantsdesignSplitsdesignTreedfactorialdiscrete.betadiscrete.gammadist.hammingdist.logDetdist.mldist.pdistanceHadamarddistinct.splitsdiversitydna2aadna2codonedQtfhmfitchgap_as_ambiguousgap_as_stategenlight2phyDatgetClansgetClipsgetDiversitygetRootgetSlicesglanceh2sth4sthadamardhas_gap_statehashkeep_as_tipKF.distlatag2n.phyDatldfactoriallentollimap_duplicatesmastmatchSplitsmaxCladeCredmccmidpointmodelTestmrca.phylomultiphyDat2pmlPartneighborNetNJnninnls.networxnnls.phylonnls.splitsnnls.treeoptim.parsimonyoptim.pmlpaceparsimonypath.distphyDatphyDat2alignmentphyDat2MultipleAlignmentplot_gamma_plus_invplotAncplotBSplotRatesplotSeqLogopmlpml_bbpml.controlpml.fitpml.freepml.initpmlClusterpmlMixpmlPartpmlPart2multiPhylopmlPenpratchetpresenceAbsencepruneTreerandom.additionratchet.controlread.nexus.distread.nexus.networxread.nexus.partitionsread.nexus.splitsread.phyDatreadDistremoveAmbiguousSitesremoveTrivialSplitsremoveUndeterminedSitesRF.distRIrNNIrSPRsankoffSH.testSiblingssimSeqSOWH.testsplitsNetworkSPR.distsprdistsuperTreesupgmathreshStateCtidytransferBootstraptreedistUNJupgmawpgmawRF.distwrite.ancestralwrite.nexus.distwrite.nexus.networxwrite.nexus.splitswrite.phyDatwrite.pmlwrite.splitswriteDist

Dependencies:apeclicpp11digestgenericsglueigraphlatticelifecyclemagrittrMatrixnlmepkgconfigquadprogRcpprlangvctrs

Ancestral Sequence Reconstruction

Rendered fromAncestral.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2024-09-09
Started: 2020-12-14

Estimating phylogenetic trees with phangorn

Rendered fromTrees.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2023-05-09
Started: 2020-12-14

Intertwining phylogenetic trees and networks: R Example Script

Rendered fromIntertwiningTreesAndNetworks.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2023-06-16
Started: 2016-04-27

Markov models and transition rate matrices

Rendered fromAdvancedFeatures.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2024-03-26
Started: 2020-12-14

Maximum likelihood by hand

Rendered fromMLbyHand.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2023-03-21
Started: 2022-11-10

Phylogenetic trees from morphological data

Rendered fromMorphological.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2023-06-20
Started: 2022-11-10

Splits and Networx

Rendered fromNetworx.Rmdusingknitr::rmarkdownon Oct 12 2024.

Last update: 2023-03-21
Started: 2015-02-01

Readme and manuals

Help Manual

Help pageTopics
Parsimony tree.acctran fitch optim.parsimony parsimony pratchet random.addition sankoff
Draw Confidences Intervals on Phylogeniesadd_boxplot add_ci
Assign and compute edge lengths from a sample of treesadd_edge_length
Add tips to a treeadd.tips
Compare splits and add support values to an objectaddConfidences addConfidences.phylo createLabel presenceAbsence
Splits representation of graphs and trees.addTrivialSplits allCircularSplits allSplits as.bitsplits.splits as.Matrix as.Matrix.splits as.matrix.splits as.phylo.splits as.prop.part.splits as.splits as.splits.bitsplits as.splits.multiPhylo as.splits.networx as.splits.phylo c.splits compatible distinct.splits matchSplits print.splits removeTrivialSplits splits unique.splits
Compute all trees topologies.allTrees
Ancestral character reconstruction.ancestral.pars ancestral.pml anc_pars anc_pml as.data.frame.ancestral as.phyDat.ancestral pace
Conversion among phylogenetic network objectsas.networx as.networx.phylo as.networx.splits networx
Likelihood of a tree.anova.pml as.pml logLik.pml optim.pml pml print.pml vcov.pml
Branch and bound for finding all most parsimonious treesbab BranchAndBound
Summaries of alignmentsbaseFreq composition_test glance.phyDat
Bootstrapbootstrap.phyDat bootstrap.pml
Chloroplast alignmentchloroplast
Consistency Index and Retention IndexCI RI
Utility function to plot.phylocladePar
Species TreecoalSpeciesTree
codonTestcodonTest
Computes a consensusNetwork from a list of trees Computes a 'networx' object from a collection of splits.consensusNet
Pairwise Distances from a Phylogenetic Networkcophenetic.networx cophenetic.splits
Computes the delta scoredelta.score
Plots a densiTree.densiTree
Compute a design matrix or non-negative LSdesignSplits designTree nnls.networx nnls.phylo nnls.splits nnls.tree
Discrete Gamma and Beta distributiondiscrete.beta discrete.gamma plotRates plot_gamma_plus_inv
Pairwise Distances from Sequencesdist.hamming dist.logDet dist.ml
Pairwise Polymorphism P-Distances from DNA Sequencesdist.p
Distance HadamarddistanceHadamard
Translate nucleic acid sequences into codonscodon2dna dna2aa dna2codon
Treat gaps as a stategap_as_ambiguous gap_as_state has_gap_state
Clans, slices and clipsdiversity getClans getClips getDiversity getSlices summary.clanistics
Tree manipulationgetRoot keep_as_tip midpoint midpoint.multiPhylo midpoint.phylo pruneTree
Hadamard Matrices and Fast Hadamard Multiplicationfhm h2st h4st hadamard
Identify splits in a networkidentify.networx
Plot of a Sequence Alignmentimage.phyDat
Replace leading and trailing alignment gaps with an ambiguous statelatag2n.phyDat
Laurasiatherian data (AWCMEE)Laurasiatherian
Arithmetic Operatorsdfactorial ldfactorial
Lento plotlento
Internal maximum likelihood functions.edQt lli pml.fit pml.free pml.init
Maximum agreement subtreemast
Maximum clade credibility treeallCompat maxCladeCred mcc
Morphological characters of Mites (Schäffer et al. 2010)mites
ModelTestAICc modelTest
Partition model.multiphyDat2pmlPart pmlPart pmlPart2multiPhylo
Computes a neighborNet from a distance matrixneighborNet
Neighbor-JoiningNJ UNJ
Tree rearrangements.nni rNNI rSPR
Conversion among Sequence Formatsacgt2ry as.AAbin.phyDat as.character.phyDat as.data.frame.phyDat as.DNAbin.phyDat as.MultipleAlignment as.MultipleAlignment.phyDat as.phyDat as.phyDat.AAbin as.phyDat.AAStringSet as.phyDat.alignment as.phyDat.character as.phyDat.data.frame as.phyDat.DNAbin as.phyDat.DNAStringSet as.phyDat.factor as.phyDat.matrix as.phyDat.MultipleAlignment as.StringSet as.StringSet.phyDat genlight2phyDat phyDat phyDat2alignment phyDat2MultipleAlignment
plot phylogenetic networksplot.networx
Plot phylogeny of a pml objectplot.pml
Plot ancestral character on a treeadd_mutations plotAnc plotSeqLogo
Plotting trees with bootstrap valuesadd_support plotBS
Likelihood of a tree.pml_bb
Auxiliary for Controlling Fittingpml.control ratchet.control
Stochastic PartitioningpmlCluster
Phylogenetic mixture modelpmlMix
Generic functions for class phyDatallSitePattern c.phyDat cbind.phyDat print.phyDat removeAmbiguousSites removeUndeterminedSites subset.phyDat unique.phyDat [.phyDat
Function to import partitioned data from nexus filesread.nexus.partitions
Function to import and export splits and networksread.nexus.networx read.nexus.splits write.nexus.networx write.nexus.splits write.splits
Import and export sequence alignmentsread.phyDat write.phyDat
Shimodaira-Hasegawa TestSH.test
Simulate sequences.simSeq simSeq.phylo simSeq.pml
Swofford-Olsen-Waddell-Hillis TestSOWH.test
Phylogenetic NetworksplitsNetwork
Super Tree methodssuperTree
Transfer BootstraptransferBootstrap
Distances between treesKF.dist path.dist RF.dist SPR.dist sprdist treedist wRF.dist
UPGMA, WPGMA and sUPGMAsupgma upgma wpgma
Export and convenience functions for ancestral reconstructionsas.ancestral print.ancestral write.ancestral
Export pml objectswrite.pml
Writing and reading distances in phylip and nexus formatread.nexus.dist readDist unique.dist write.nexus.dist writeDist
Yeast alignment (Rokas et al.)yeast