Man pages for KlausVigo/phangorn
Phylogenetic Reconstruction and Analysis
| add_ci | Draw Confidences Intervals on Phylogenies |
| addConfidences | Compare splits and add support values to an object |
| add_edge_length | Assign and compute edge lengths from a sample of trees |
| add.tips | Add tips to a tree |
| allTrees | Compute all trees topologies. |
| Ancestors | tree utility function |
| ancestral.pml | Ancestral character reconstruction. |
| as.networx | Conversion among phylogenetic network objects |
| as.phyDat | Conversion among Sequence Formats |
| as.splits | Splits representation of graphs and trees. |
| bab | Branch and bound for finding all most parsimonious trees |
| baseFreq | Summaries of alignments |
| bootstrap.pml | Bootstrap |
| chloroplast | Chloroplast alignment |
| CI | Consistency Index and Retention Index |
| cladePar | Utility function to plot.phylo |
| coalSpeciesTree | Species Tree |
| codonTest | codonTest |
| consensusNet | Computes a consensusNetwork from a list of trees Computes a... |
| cophenetic.networx | Pairwise Distances from a Phylogenetic Network |
| delta.score | Computes the delta score |
| densiTree | Plots a densiTree. |
| designTree | Compute a design matrix or non-negative LS |
| dfactorial | Arithmetic Operators |
| discrete.gamma | Discrete Gamma and Beta distribution |
| distanceHadamard | Distance Hadamard |
| dist.hamming | Pairwise Distances from Sequences |
| dist.p | Pairwise Polymorphism P-Distances from DNA Sequences |
| dna2codon | Translate nucleic acid sequences into codons |
| gap_as_state | Treat gaps as a state |
| getClans | Clans, slices and clips |
| hadamard | Hadamard Matrices and Fast Hadamard Multiplication |
| identify.networx | Identify splits in a network |
| image.phyDat | Plot of a Sequence Alignment |
| Laurasiatherian | Laurasiatherian data (AWCMEE) |
| lento | Lento plot |
| ltg2amb | Replace leading and trailing alignment gaps with an ambiguous... |
| mast | Maximum agreement subtree |
| maxCladeCred | Maximum clade credibility tree |
| midpoint | Tree manipulation |
| mites | Morphological characters of Mites (Schäffer et al. 2010) |
| modelTest | ModelTest |
| neighborNet | Computes a neighborNet from a distance matrix |
| NJ | Neighbor-Joining |
| nni | Tree rearrangements. |
| parsimony | Parsimony tree. |
| phangorn-internal | Internal phangorn Functions |
| phangorn-package | phangorn: Phylogenetic Reconstruction and Analysis |
| phyDat | Generic functions for class phyDat |
| plot.ancestral | Plot ancestral character on a tree |
| plotBS | Plotting trees with bootstrap values |
| plot.networx | plot phylogenetic networks |
| plot.pml | Plot phylogeny of a pml object |
| pml | Likelihood of a tree. |
| pml_bb | Likelihood of a tree. |
| pmlCluster | Stochastic Partitioning |
| pml.control | Auxiliary for Controlling Fitting |
| pml.fit | Internal maximum likelihood functions. |
| pmlMix | Phylogenetic mixture model |
| pmlPart | Partition model. |
| read.nexus.partitions | Function to import partitioned data from nexus files |
| read.nexus.splits | Function to import and export splits and networks |
| read.phyDat | Import and export sequence alignments |
| reexports | Objects exported from other packages |
| SH.test | Shimodaira-Hasegawa Test |
| simSeq | Simulate sequences. |
| SOWH.test | Swofford-Olsen-Waddell-Hillis Test |
| splitsNetwork | Phylogenetic Network |
| superTree | Super Tree methods |
| transferBootstrap | Transfer Bootstrap |
| treedist | Distances between trees |
| upgma | UPGMA, WPGMA and sUPGMA |
| write.ancestral | Export and convenience functions for ancestral... |
| writeDist | Writing and reading distances in phylip and nexus format |
| write.pml | Export pml objects |
| yeast | Yeast alignment (Rokas et al.) |
