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| phyloch-package | Phylogenetic Data Analysis And Display |
| add.geoscale | Geological Time Scale for Phylogenies |
| add.timeframe | High-lighting ages in chronograms |
| add.trendline | Plotting Trendlines on a Phylogeny |
| aliscore | Cleaning of Sequence Alignments |
| append2tips | Append Symbols or Text to Tip Labels |
| axisChrono | Axis for time-calibrated phylogenies |
| axisGeo | Geological Time Axis for Time-Calibrated Phylogenies |
| box.clades | Plot Boxes around Clades in a Phylogeny |
| box.tips | Plot Boxes around Clades in a Phylogeny |
| c.alignment | Concatenation of DNA Sequences |
| c.genes | Concatenation of DNA Sequences |
| clade.bars | Plot Bars beside Clades in a Phylogeny |
| code.simple.gaps | Simple Gap/Indel Coding |
| compare.phylo | Compare PHYLO Objects Graphically |
| continousML | ML Estimation of Continous Traits |
| delete.empty.cells | Delete empty rows and columns from a DNA sequence alignment |
| delete.gaps | Remove Indel Positions from an Alignment |
| descendants | Descendants of an Internal Node in a Phylogeny |
| drop.tip2 | Remove Tips from a Phylogenetic Tree |
| edge.color | Colors for Tips and Edges in Phylogenies |
| extract.clade2 | Extract Clades from a Phylogentic Tree |
| fillEndsWithN | Fill alignment ends with N |
| fixNodes | Standard Node Numbering in Phylo Objects |
| gblocks | Cleaning of Sequence Alignments |
| geophylo | 3D Geophylogenies for GIS Applications |
| gradstein04 | Stratigraphic Chart 2004 |
| homogen.base.freq | Homogeneity of base frequencies |
| hordeum | Phylogeny of Wild Barley (Hordeum) |
| HPDbars | Plot HPD Intervals on Time-calibrated Phylogenies |
| ident.seq | Identify or delete identical DNA sequences |
| mafft | DNA Sequence Alignment with MAFFT |
| mrbayes | Bayesian MCMC Tree Search with MrBayes |
| mrbayes.mixed | Bayesian MCMC Tree Search with MrBayes |
| multistate | MULTISTATE |
| multistateMCMC | MULTISTATE |
| multistateML | MULTISTATE |
| node.support | Visualizing Node Support on Phylogenetic Trees |
| node.trans | Translate Internal Node Indices between Trees |
| nodeInfo | Graphical Annotation of Internal Nodes |
| noi | Identification of MRCAs for Taxon Sets |
| origin | Phylogenetic Trees of True Vipers |
| phyloch | Phylogenetic Data Analysis And Display |
| pis | Number of parsimony-informative sites |
| plot.phylo.upon | Helper function |
| plotNetwork | Plot Haplotype/Genotype Networks |
| prank | PRANK |
| raxml | Maximium Likelihood Tree Search |
| rbeauti | XML Input Files for BEAST |
| read.beast | Read Bayesian Trees |
| read.beast.table | Extract node data from BEAST chronogram |
| read.fas | Read DNA Sequences |
| read.mrbayes | Read Bayesian Trees |
| read.nex | Read DNA Sequences |
| read.phy | Read DNA Sequences |
| read.starbeast | Read Bayesian Trees |
| rotate2 | Swapping Sister Clades |
| shiftNodeAge | Modify Node Ages in Ultramtric Trees |
| sister | Identification of Sister Nodes and Clades |
| strat2012 | Stratigraphic Chart 2012 |
| string.dim | Dimensions of Rotated Strings |
| taxo.fonts | Font Types for Tip Labels |
| tip.color | Colors for Tips and Edges in Phylogenies |
| vipera | Phylogenetic Trees of True Vipers |
| vipera.bayes | Phylogenetic Trees of True Vipers |
| vipera.ml | Phylogenetic Trees of True Vipers |
| viperidae | Phylogenetic Trees of True Vipers |
| write.fas | Write DNA Sequences to File |
| write.nex | Write DNA Sequences to File |
| write.partitioned.nex | Write partitioned and commented NEXUS files |
| write.phy | Write DNA Sequences to File |