A B C D E F G H L M N O P R S T U W Y
| phangorn-package | Phylogenetic analysis in R |
| acctran | Parsimony tree. |
| acgt2ry | Conversion among Sequence Formats |
| addConfidences | Compare splits and add support values to an object |
| addTrivialSplits | Splits representation of graphs and trees. |
| AICc | ModelTest |
| allSitePattern | Conversion among Sequence Formats |
| allSplits | Splits representation of graphs and trees. |
| allTrees | Compute all trees topologies. |
| Ancestors | tree utility function |
| ancestral.pars | Ancestral character reconstruction. |
| ancestral.pml | Ancestral character reconstruction. |
| 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.phyDat | Conversion among Sequence Formats |
| as.networx | Phylogenetic networks |
| as.networx.splits | Phylogenetic networks |
| as.phyDat | Conversion among Sequence Formats |
| as.phyDat.alignment | Conversion among Sequence Formats |
| as.phyDat.DNAbin | Conversion among Sequence Formats |
| as.phyDat.MultipleAlignment | Conversion among Sequence Formats |
| as.phylo.splits | Splits representation of graphs and trees. |
| as.prop.part.splits | Splits representation of graphs and trees. |
| as.splits | 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. |
| bab | Branch and bound for finding all most parsimonious trees |
| baseFreq | Conversion among Sequence Formats |
| bootstrap.phyDat | Bootstrap |
| bootstrap.pml | Bootstrap |
| BranchAndBound | Branch and bound for finding all most parsimonious trees |
| c.phyDat | Conversion among Sequence Formats |
| cbind.phyDat | Conversion among Sequence Formats |
| Children | tree utility function |
| chloroplast | Chloroplast alignment |
| CI | Parsimony tree. |
| cladePar | Utility function to plot.phylo |
| coalSpeciesTree | Super Tree and Species Tree methods |
| 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 |
| countCycles | Splits representation of graphs and trees. |
| delta.score | Computes the delta score |
| densiTree | Plots a densiTree. |
| Descendants | tree utility function |
| designSplits | Compute a design matrix or non-negative LS |
| designTree | Compute a design matrix or non-negative LS |
| dfactorial | Arithmetic Operators |
| discrete.gamma | Internal maximum likelihood functions. |
| 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 |
| diversity | Clans, slices and clips |
| edQt | Internal maximum likelihood functions. |
| fhm | Hadamard Matrices and Fast Hadamard Multiplication |
| fitch | Parsimony tree. |
| getClans | Clans, slices and clips |
| getClips | Clans, slices and clips |
| getDiversity | Clans, slices and clips |
| getRoot | Tree manipulation |
| getSlices | Clans, slices and clips |
| h2st | Hadamard Matrices and Fast Hadamard Multiplication |
| h4st | Hadamard Matrices and Fast Hadamard Multiplication |
| hadamard | Hadamard Matrices and Fast Hadamard Multiplication |
| Laurasiatherian | Laurasiatherian data (AWCMEE) |
| ldfactorial | Arithmetic Operators |
| lento | Lento plot |
| lli | Internal maximum likelihood functions. |
| midpoint | Tree manipulation |
| modelTest | ModelTest |
| mrca.phylo | tree utility function |
| neighborNet | Computes a neighborNet from a distance matrix |
| 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 |
| optim.parsimony | Parsimony tree. |
| optim.pml | Likelihood of a tree. |
| pace | Ancestral character reconstruction. |
| parsimony | Parsimony tree. |
| phangorn | Phylogenetic analysis in R |
| phyDat | Conversion among Sequence Formats |
| phyDat2alignment | Conversion among Sequence Formats |
| phyDat2MultipleAlignment | Conversion among Sequence Formats |
| plot.networx | Phylogenetic networks |
| plotAnc | Ancestral character reconstruction. |
| plotBS | Bootstrap |
| pml | Likelihood of a tree. |
| pml.control | Likelihood of a tree. |
| 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. |
| pmlPen | Phylogenetic mixture model |
| PNJ | Parsimony tree. |
| pratchet | Parsimony tree. |
| presenceAbsence | Compare splits and add support values to an object |
| print.splits | Splits representation of graphs and trees. |
| pruneTree | Tree manipulation |
| random.addition | Parsimony tree. |
| read.aa | Read Amino Acid Sequences in a File |
| read.nexus.splits | Splits representation of graphs and trees. |
| read.phyDat | Conversion among Sequence Formats |
| readDist | Pairwise Distances from Sequences |
| removeUndeterminedSites | Conversion among Sequence Formats |
| RF.dist | Distances between trees |
| RI | Parsimony tree. |
| rNNI | Tree rearrangements. |
| rSPR | Tree rearrangements. |
| sankoff | Parsimony tree. |
| SH.test | Shimodaira-Hasegawa Test |
| Siblings | tree utility function |
| simSeq | Simulate sequences. |
| simSeq.phylo | Simulate sequences. |
| simSeq.pml | Simulate sequences. |
| SOWH.test | Swofford-Olsen-Waddell-Hillis Test |
| splitsNetwork | Phylogenetic Network |
| subset.phyDat | Conversion among Sequence Formats |
| superTree | Super Tree and Species Tree methods |
| treedist | Distances between trees |
| unique.phyDat | Conversion among Sequence Formats |
| UNJ | Neighbor-Joining |
| upgma | UPGMA and WPGMA |
| wpgma | UPGMA and WPGMA |
| write.nexus.splits | Splits representation of graphs and trees. |
| write.phyDat | Conversion among Sequence Formats |
| write.splits | Splits representation of graphs and trees. |
| writeDist | Pairwise Distances from Sequences |
| yeast | Yeast alignment (Rokas et al.) |