Package: phangorn 2.11.1
Klaus Schliep
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:
phangorn_2.11.1.tar.gz
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phangorn.pdf |phangorn.html✨
phangorn/json (API)
NEWS
| # Install 'phangorn' in R: |
| install.packages('phangorn', repos = c('https://isbool.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
softwaretechnologyqualitycontrol
Last updated 9 months agofrom:0c98e57e94. Checks:OK: 1 NOTE: 8. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 05 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 05 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 05 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 05 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 05 2024 |
Exports:acctranacgt2ryadd_boxplotadd_ciadd_edge_lengthadd.tipsaddConfidencesaddTrivialSplitsAICcallCircularSplitsallCompatallDescendantsallSitePatternallSplitsallTreesAncestorsancestral.parsancestral.pmlas.Matrixas.MultipleAlignmentas.networxas.phyDatas.pmlas.splitsbabbaseFreqbootstrap.phyDatbootstrap.pmlc.phyDatcandidate_treecbind.phyDatChildrenCIcladeParcoalSpeciesTreecodon2dnacodonTestcompatibleconsensusNetcoordscreateLabeldelta.scoredensiTreeDescendantsdesignSplitsdesignTreedfactorialdiscrete.betadiscrete.gammadist.hammingdist.logDetdist.mldist.pdistanceHadamarddistinct.splitsdiversitydna2codonedQtfhmfitchgenlight2phyDatgetClansgetClipsgetDiversitygetRootgetSlicesglanceh2sth4sthadamardhash_phyloKF.distldfactoriallentollimap_duplicatesmastmatchSplitsmaxCladeCredmccmidpointmodelTestmrca.phylomultiphyDat2pmlPartneighborNetNJnninnls.networxnnls.phylonnls.splitsnnls.treeoptim.parsimonyoptim.pmlpaceparsimonypath.distphyDatphyDat2alignmentphyDat2MultipleAlignmentplot_gamma_plus_invplotAncplotBSplotRatespmlpml_bbpml.controlpml.fitpml.freepml.initpmlClusterpmlMixpmlPartpmlPart2multiPhylopmlPenpratchetpresenceAbsencepruneTreerandom.additionratchet.controlread.aaread.nexus.distread.nexus.networxread.nexus.splitsread.phyDatreadDistremoveAmbiguousSitesremoveTrivialSplitsremoveUndeterminedSitesRF.distRIrNNIrSPRsankoffSH.testSiblingssimSeqSOWH.testsplitsNetworkSPR.distsprdistsuperTreethreshStateCtidytransferBootstraptreedistUNJupgmawpgmawRF.distwrite.nexus.distwrite.nexus.networxwrite.nexus.splitswrite.phyDatwrite.splitswriteDist
Dependencies:apeclicpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmepkgconfigquadprogRcpprlangvctrs
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 pace plotAnc |
| Conversion among phylogenetic network objects | as.networx as.networx.phylo as.networx.splits networx |
| Likelihood of a tree. | as.pml optim.pml pml |
| Branch and bound for finding all most parsimonious trees | bab BranchAndBound |
| Summaries of alignments | baseFreq 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 dna2codon |
| Clans, slices and clips | diversity getClans getClips getDiversity getSlices summary.clanistics |
| Tree manipulation | getRoot 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 |
| 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.alignment as.phyDat.character as.phyDat.data.frame as.phyDat.DNAbin as.phyDat.factor as.phyDat.matrix as.phyDat.MultipleAlignment genlight2phyDat phyDat phyDat2alignment phyDat2MultipleAlignment |
| plot phylogenetic networks | plot.networx |
| Plotting trees with bootstrap values | 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 removeAmbiguousSites removeUndeterminedSites subset.phyDat unique.phyDat [.phyDat |
| Read Amino Acid Sequences in a File | read.aa |
| 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 and WPGMA | upgma wpgma |
| 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 |
