Phylogenetic Reconstruction and Analysis
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Documentation for package ‘phangorn’ version 2.11.1
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A B C D E F G H I K L M N O P R S T U W Y misc
-- A --
| acctran | Parsimony tree. |
| acgt2ry | Conversion among Sequence Formats |
| add.tips | Add tips to a tree |
| addConfidences | Compare splits and add support values to an object |
| addConfidences.phylo | Compare splits and add support values to an object |
| addTrivialSplits | Splits representation of graphs and trees. |
| add_boxplot | Draw Confidences Intervals on Phylogenies |
| add_ci | Draw Confidences Intervals on Phylogenies |
| add_edge_length | Assign and compute edge lengths from a sample of trees |
| AICc | ModelTest |
| allCircularSplits | Splits representation of graphs and trees. |
| allCompat | Maximum clade credibility tree |
| allSitePattern | Generic functions for class phyDat |
| allSplits | Splits representation of graphs and trees. |
| allTrees | Compute all trees topologies. |
| ancestral.pars | Ancestral character reconstruction. |
| ancestral.pml | Ancestral character reconstruction. |
| as.AAbin.phyDat | Conversion among Sequence Formats |
| as.bitsplits.splits | Splits representation of graphs and trees. |
| as.character.phyDat | Conversion among Sequence Formats |
| as.data.frame.phyDat | Conversion among Sequence Formats |
| as.DNAbin.phyDat | Conversion among Sequence Formats |
| as.Matrix | Splits representation of graphs and trees. |
| as.Matrix.splits | Splits representation of graphs and trees. |
| as.matrix.splits | Splits representation of graphs and trees. |
| as.MultipleAlignment | Conversion among Sequence Formats |
| as.MultipleAlignment.phyDat | Conversion among Sequence Formats |
| as.networx | Conversion among phylogenetic network objects |
| as.networx.phylo | Conversion among phylogenetic network objects |
| as.networx.splits | Conversion among phylogenetic network objects |
| as.phyDat | Conversion among Sequence Formats |
| as.phyDat.alignment | Conversion among Sequence Formats |
| as.phyDat.character | Conversion among Sequence Formats |
| as.phyDat.data.frame | Conversion among Sequence Formats |
| as.phyDat.DNAbin | Conversion among Sequence Formats |
| as.phyDat.factor | Conversion among Sequence Formats |
| as.phyDat.matrix | Conversion among Sequence Formats |
| as.phyDat.MultipleAlignment | Conversion among Sequence Formats |
| as.phylo.splits | Splits representation of graphs and trees. |
| as.pml | Likelihood of a tree. |
| as.prop.part.splits | Splits representation of graphs and trees. |
| as.splits | Splits representation of graphs and trees. |
| as.splits.bitsplits | Splits representation of graphs and trees. |
| as.splits.multiPhylo | Splits representation of graphs and trees. |
| as.splits.networx | Splits representation of graphs and trees. |
| as.splits.phylo | Splits representation of graphs and trees. |
-- B --
| bab | Branch and bound for finding all most parsimonious trees |
| baseFreq | Summaries of alignments |
| bootstrap.phyDat | Bootstrap |
| bootstrap.pml | Bootstrap |
| BranchAndBound | Branch and bound for finding all most parsimonious trees |
-- C --
| c.phyDat | Generic functions for class phyDat |
| c.splits | Splits representation of graphs and trees. |
| cbind.phyDat | Generic functions for class phyDat |
| chloroplast | Chloroplast alignment |
| CI | Consistency Index and Retention Index |
| cladePar | Utility function to plot.phylo |
| coalSpeciesTree | Species Tree |
| codon2dna | Translate nucleic acid sequences into codons |
| codonTest | codonTest |
| compatible | Splits representation of graphs and trees. |
| consensusNet | Computes a consensusNetwork from a list of trees Computes a 'networx' object from a collection of splits. |
| cophenetic.networx | Pairwise Distances from a Phylogenetic Network |
| cophenetic.splits | Pairwise Distances from a Phylogenetic Network |
| createLabel | Compare splits and add support values to an object |
-- D --
| delta.score | Computes the delta score |
| densiTree | Plots a densiTree. |
| designSplits | Compute a design matrix or non-negative LS |
| designTree | Compute a design matrix or non-negative LS |
| dfactorial | Arithmetic Operators |
| discrete.beta | Discrete Gamma and Beta distribution |
| discrete.gamma | Discrete Gamma and Beta distribution |
| dist.hamming | Pairwise Distances from Sequences |
| dist.logDet | Pairwise Distances from Sequences |
| dist.ml | Pairwise Distances from Sequences |
| dist.p | Pairwise Polymorphism P-Distances from DNA Sequences |
| distanceHadamard | Distance Hadamard |
| distinct.splits | Splits representation of graphs and trees. |
| diversity | Clans, slices and clips |
| dna2codon | Translate nucleic acid sequences into codons |
-- E --
| edQt | Internal maximum likelihood functions. |
-- F --
| fhm | Hadamard Matrices and Fast Hadamard Multiplication |
| fitch | Parsimony tree. |
-- G --
| genlight2phyDat | Conversion among Sequence Formats |
| getClans | Clans, slices and clips |
| getClips | Clans, slices and clips |
| getDiversity | Clans, slices and clips |
| getRoot | Tree manipulation |
| getSlices | Clans, slices and clips |
| glance.phyDat | Summaries of alignments |
-- H --
| h2st | Hadamard Matrices and Fast Hadamard Multiplication |
| h4st | Hadamard Matrices and Fast Hadamard Multiplication |
| hadamard | Hadamard Matrices and Fast Hadamard Multiplication |
-- I --
| identify.networx | Identify splits in a network |
| image.phyDat | Plot of a Sequence Alignment |
-- K --
| KF.dist | Distances between trees |
-- L --
| Laurasiatherian | Laurasiatherian data (AWCMEE) |
| ldfactorial | Arithmetic Operators |
| lento | Lento plot |
| lli | Internal maximum likelihood functions. |
-- M --
| mast | Maximum agreement subtree |
| matchSplits | Splits representation of graphs and trees. |
| maxCladeCred | Maximum clade credibility tree |
| mcc | Maximum clade credibility tree |
| midpoint | Tree manipulation |
| midpoint.multiPhylo | Tree manipulation |
| midpoint.phylo | Tree manipulation |
| mites | Morphological characters of Mites (Schäffer et al. 2010) |
| modelTest | ModelTest |
| multiphyDat2pmlPart | Partition model. |
-- N --
| neighborNet | Computes a neighborNet from a distance matrix |
| networx | Conversion among phylogenetic network objects |
| NJ | Neighbor-Joining |
| nni | Tree rearrangements. |
| nnls.networx | Compute a design matrix or non-negative LS |
| nnls.phylo | Compute a design matrix or non-negative LS |
| nnls.splits | Compute a design matrix or non-negative LS |
| nnls.tree | Compute a design matrix or non-negative LS |
-- O --
| optim.parsimony | Parsimony tree. |
| optim.pml | Likelihood of a tree. |
-- P --
| pace | Ancestral character reconstruction. |
| parsimony | Parsimony tree. |
| path.dist | Distances between trees |
| phyDat | Conversion among Sequence Formats |
| phyDat2alignment | Conversion among Sequence Formats |
| phyDat2MultipleAlignment | Conversion among Sequence Formats |
| plot.networx | plot phylogenetic networks |
| plotAnc | Ancestral character reconstruction. |
| plotBS | Plotting trees with bootstrap values |
| plotRates | Discrete Gamma and Beta distribution |
| plot_gamma_plus_inv | Discrete Gamma and Beta distribution |
| pml | Likelihood of a tree. |
| pml.control | Auxiliary for Controlling Fitting |
| pml.fit | Internal maximum likelihood functions. |
| pml.free | Internal maximum likelihood functions. |
| pml.init | Internal maximum likelihood functions. |
| pmlCluster | Stochastic Partitioning |
| pmlMix | Phylogenetic mixture model |
| pmlPart | Partition model. |
| pmlPart2multiPhylo | Partition model. |
| pml_bb | Likelihood of a tree. |
| pratchet | Parsimony tree. |
| presenceAbsence | Compare splits and add support values to an object |
| print.phyDat | Generic functions for class phyDat |
| print.splits | Splits representation of graphs and trees. |
| pruneTree | Tree manipulation |
-- R --
| random.addition | Parsimony tree. |
| ratchet.control | Auxiliary for Controlling Fitting |
| read.aa | Read Amino Acid Sequences in a File |
| read.nexus.dist | Writing and reading distances in phylip and nexus format |
| read.nexus.networx | Function to import and export splits and networks |
| read.nexus.splits | Function to import and export splits and networks |
| read.phyDat | Import and export sequence alignments |
| readDist | Writing and reading distances in phylip and nexus format |
| removeAmbiguousSites | Generic functions for class phyDat |
| removeTrivialSplits | Splits representation of graphs and trees. |
| removeUndeterminedSites | Generic functions for class phyDat |
| RF.dist | Distances between trees |
| RI | Consistency Index and Retention Index |
| rNNI | Tree rearrangements. |
| rSPR | Tree rearrangements. |
-- S --
| sankoff | Parsimony tree. |
| SH.test | Shimodaira-Hasegawa Test |
| simSeq | Simulate sequences. |
| simSeq.phylo | Simulate sequences. |
| simSeq.pml | Simulate sequences. |
| SOWH.test | Swofford-Olsen-Waddell-Hillis Test |
| splits | Splits representation of graphs and trees. |
| splitsNetwork | Phylogenetic Network |
| SPR.dist | Distances between trees |
| sprdist | Distances between trees |
| subset.phyDat | Generic functions for class phyDat |
| summary.clanistics | Clans, slices and clips |
| superTree | Super Tree methods |
-- T --
| transferBootstrap | Transfer Bootstrap |
| treedist | Distances between trees |
-- U --
| unique.dist | Writing and reading distances in phylip and nexus format |
| unique.phyDat | Generic functions for class phyDat |
| unique.splits | Splits representation of graphs and trees. |
| UNJ | Neighbor-Joining |
| upgma | UPGMA and WPGMA |
-- W --
| wpgma | UPGMA and WPGMA |
| wRF.dist | Distances between trees |
| write.nexus.dist | Writing and reading distances in phylip and nexus format |
| write.nexus.networx | Function to import and export splits and networks |
| write.nexus.splits | Function to import and export splits and networks |
| write.phyDat | Import and export sequence alignments |
| write.splits | Function to import and export splits and networks |
| writeDist | Writing and reading distances in phylip and nexus format |
-- Y --
| yeast | Yeast alignment (Rokas et al.) |
-- misc --
| [.phyDat | Generic functions for class phyDat |