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:
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phangorn.pdf |phangorn.html✨
phangorn/json (API)
NEWS
| # Install 'phangorn' in R: |
| install.packages('phangorn', repos = c('https://klausvigo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/klausvigo/phangorn/issues
- Laurasiatherian - Laurasiatherian data
- chloroplast - Chloroplast alignment
- mites - Morphological characters of Mites
- yeast - Yeast alignment
softwaretechnologyqualitycontrolphylogenetic-analysisphylogenetics
Last updated 1 days agofrom:7e27429101. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win-x86_64 | OK | Nov 20 2024 |
| R-4.5-linux-x86_64 | OK | Nov 20 2024 |
| R-4.4-win-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-aarch64 | OK | Nov 20 2024 |
| R-4.3-win-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-aarch64 | OK | Nov 20 2024 |
Exports:acctranacgt2ryadd_boxplotadd_ciadd_edge_lengthadd_mutationsadd_supportadd.tipsaddConfidencesaddTrivialSplitsAICcallCircularSplitsallCompatallDescendantsallSitePatternallSplitsallTreesanc_parsanc_pmlAncestorsancestral.parsancestral.pmlas.ancestralas.Matrixas.MultipleAlignmentas.networxas.phyDatas.pmlas.splitsas.StringSetbabbaseFreqbootstrap.phyDatbootstrap.pmlcandidate_treeChildrenCIcladeParcoalSpeciesTreecodon2dnacodonTestcompatiblecomposition_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.distsprdistsuperTreesupgmathreshStateCtransferBootstraptreedistUNJupgmawpgmawRF.distwrite.ancestralwrite.nexus.distwrite.nexus.networxwrite.nexus.splitswrite.phyDatwrite.pmlwrite.splitswriteDist
Dependencies:apeclicpp11digestgenericsglueigraphlatticelifecyclemagrittrMatrixnlmepkgconfigquadprogRcppRcppArmadillorlangvctrs
Ancestral Sequence Reconstruction
Rendered fromAncestral.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2024-10-18
Started: 2020-12-14
Estimating phylogenetic trees with phangorn
Rendered fromTrees.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2024-11-04
Started: 2020-12-14
Intertwining phylogenetic trees and networks: R Example Script
Rendered fromIntertwiningTreesAndNetworks.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2023-06-16
Started: 2016-04-27
Markov models and transition rate matrices
Rendered fromAdvancedFeatures.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2024-03-26
Started: 2020-12-14
Maximum likelihood by hand
Rendered fromMLbyHand.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2023-03-21
Started: 2022-11-10
Phylogenetic trees from morphological data
Rendered fromMorphological.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2023-06-20
Started: 2022-11-10
Splits and Networx
Rendered fromNetworx.Rmdusingknitr::rmarkdownon Nov 20 2024.Last update: 2023-03-21
Started: 2015-02-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Parsimony tree. | acctran fitch optim.parsimony parsimony pratchet random.addition sankoff |
| Draw Confidences Intervals on Phylogenies | add_boxplot add_ci |
| Assign and compute edge lengths from a sample of trees | add_edge_length |
| Add tips to a tree | add.tips |
| Compare splits and add support values to an object | addConfidences 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 pace |
| Conversion among phylogenetic network objects | as.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 trees | bab BranchAndBound |
| Summaries of alignments | baseFreq composition_test glance.phyDat |
| Bootstrap | bootstrap.phyDat bootstrap.pml |
| Chloroplast alignment | chloroplast |
| Consistency Index and Retention Index | CI RI |
| Utility function to plot.phylo | cladePar |
| Species Tree | coalSpeciesTree |
| codonTest | codonTest |
| Computes a consensusNetwork from a list of trees Computes a 'networx' object from a collection of splits. | consensusNet |
| Pairwise Distances from a Phylogenetic Network | cophenetic.networx cophenetic.splits |
| Computes the delta score | delta.score |
| Plots a densiTree. | densiTree |
| Compute a design matrix or non-negative LS | designSplits designTree nnls.networx nnls.phylo nnls.splits nnls.tree |
| Discrete Gamma and Beta distribution | discrete.beta discrete.gamma plotRates plot_gamma_plus_inv |
| Pairwise Distances from Sequences | dist.hamming dist.logDet dist.ml |
| Pairwise Polymorphism P-Distances from DNA Sequences | dist.p |
| Distance Hadamard | distanceHadamard |
| Translate nucleic acid sequences into codons | codon2dna dna2aa dna2codon |
| Treat gaps as a state | gap_as_ambiguous gap_as_state has_gap_state |
| Clans, slices and clips | diversity getClans getClips getDiversity getSlices summary.clanistics |
| Tree manipulation | getRoot keep_as_tip midpoint midpoint.multiPhylo midpoint.phylo pruneTree |
| Hadamard Matrices and Fast Hadamard Multiplication | fhm h2st h4st hadamard |
| Identify splits in a network | identify.networx |
| Plot of a Sequence Alignment | image.phyDat |
| Replace leading and trailing alignment gaps with an ambiguous state | latag2n.phyDat |
| Laurasiatherian data (AWCMEE) | Laurasiatherian |
| Arithmetic Operators | dfactorial ldfactorial |
| Lento plot | lento |
| Internal maximum likelihood functions. | edQt lli pml.fit pml.free pml.init |
| Maximum agreement subtree | mast |
| Maximum clade credibility tree | allCompat maxCladeCred mcc |
| Morphological characters of Mites (Schäffer et al. 2010) | mites |
| ModelTest | AICc modelTest |
| Partition model. | multiphyDat2pmlPart pmlPart pmlPart2multiPhylo |
| Computes a neighborNet from a distance matrix | neighborNet |
| Neighbor-Joining | NJ UNJ |
| Tree rearrangements. | nni rNNI rSPR |
| Conversion among Sequence Formats | acgt2ry 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 networks | plot.networx |
| Plot phylogeny of a pml object | plot.pml |
| Plot ancestral character on a tree | add_mutations plotAnc plotSeqLogo |
| Plotting trees with bootstrap values | add_support plotBS |
| Likelihood of a tree. | pml_bb |
| Auxiliary for Controlling Fitting | pml.control ratchet.control |
| Stochastic Partitioning | pmlCluster |
| Phylogenetic mixture model | pmlMix |
| Generic functions for class phyDat | allSitePattern c.phyDat cbind.phyDat print.phyDat rbind.phyDat removeAmbiguousSites removeUndeterminedSites subset.phyDat unique.phyDat [.phyDat |
| Function to import partitioned data from nexus files | read.nexus.partitions |
| Function to import and export splits and networks | read.nexus.networx read.nexus.splits write.nexus.networx write.nexus.splits write.splits |
| Import and export sequence alignments | read.phyDat write.phyDat |
| Shimodaira-Hasegawa Test | SH.test |
| Simulate sequences. | simSeq simSeq.phylo simSeq.pml |
| Swofford-Olsen-Waddell-Hillis Test | SOWH.test |
| Phylogenetic Network | splitsNetwork |
| Super Tree methods | superTree |
| Transfer Bootstrap | transferBootstrap |
| Distances between trees | KF.dist path.dist RF.dist SPR.dist sprdist treedist wRF.dist |
| UPGMA, WPGMA and sUPGMA | supgma upgma wpgma |
| Export and convenience functions for ancestral reconstructions | as.ancestral as.data.frame.ancestral as.phyDat.ancestral print.ancestral write.ancestral |
| Export pml objects | write.pml |
| Writing and reading distances in phylip and nexus format | read.nexus.dist readDist unique.dist write.nexus.dist writeDist |
| Yeast alignment (Rokas et al.) | yeast |
