Phylogenetic Tools for Comparative Biology (and Other Things)
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Documentation for package ‘phytools’ version 2.1-1
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A B C D E F G H K L M N O P R S T U V W
| phytools-package | phytools: Phylogenetic Tools for comparative biology (and other things) |
-- A --
| add.arrow | Add an arrow pointing to a tip or node on the tree |
| add.color.bar | Add color bar to a plot |
| add.everywhere | Add tip to all edges in a tree |
| add.random | Add tips at random to the tree |
| add.simmap.legend | Add legend to stochastically mapped tree |
| add.species.to.genus | Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree |
| aic.w | Computes Akaike weights |
| allFurcTrees | Generate all bi- and multifurcating unrooted trees |
| allRotations | Rotates a node or set of nodes in a phylogenetic tree |
| anc.Bayes | Bayesian ancestral character estimation |
| anc.ML | Ancestral character estimation using likelihood |
| anc.trend | Ancestral character estimation with a trend |
| ancr | Compute marginal or joint ancestral state estimates |
| ancThresh | Ancestral character estimation under the threshold model using Bayesian MCMC |
| anole.data | Phylogenetic datasets |
| anoletree | Phylogenetic datasets |
| ansi_phylo | Compute the parsimony score |
| ant.geog | Phylogenetic datasets |
| ant.tree | Phylogenetic datasets |
| applyBranchLengths | Applies the branch lengths of a reference tree to a target |
| arc.cladelabels | Add labels to subtrees of a plotted phylogeny |
| as.multiPhylo | Conversion to object of class '"multiPhylo"' |
| as.multiPhylo.multiSimmap | Conversion to object of class '"multiPhylo"' |
| as.multiPhylo.phylo | Conversion to object of class '"multiPhylo"' |
| as.prcomp | Phylogenetic principal components analysis |
| as.princomp | Phylogenetic principal components analysis |
| as.Qmatrix | Convert a fitted M_k_ model to a Q-matrix |
| as.Qmatrix.fitMk | Convert a fitted M_k_ model to a Q-matrix |
| ave.rates | Average the posterior rates |
| averageTree | Compute an average tree from a set of trees and related operations |
-- B --
| backbone.toPhylo | Converts tree to backbone or vice versa |
| bat.tree | Phylogenetic datasets |
| bat_virus.data | Phylogenetic datasets |
| bd | Convert object of class '"birthdeath"' to raw birth & death rates |
| betaCoV.tree | Phylogenetic datasets |
| bind.tip | Attaches a new tip to a tree |
| bind.tree.simmap | Binds two trees of class '"simmap"' |
| biplot.phyl.pca | Phylogenetic principal components analysis |
| bmPlot | Simulates and visualizes discrete-time Brownian evolution on a phylogeny |
| bonyfish.data | Phylogenetic datasets |
| bonyfish.tree | Phylogenetic datasets |
| branching.diffusion | Animation of branching random diffusion |
| brownie.lite | Likelihood test for rate variation in a continuous trait |
| brownieREML | REML version of brownie.lite |
| butterfly.data | Phylogenetic datasets |
| butterfly.tree | Phylogenetic datasets |
-- C --
| cladelabels | Add labels to subtrees of a plotted phylogeny |
| coef.phyl.RMA | Phylogenetic reduced major axis (RMA) regression |
| collapse.to.star | Collapse a subtree to a star phylogeny |
| collapseTree | Interactive tree visualizer |
| compare.chronograms | Compares two chronograms with precisely matching nodes in a visual manner |
| compute.mr | Matrix representation parsimony supertree estimation |
| consensus.edges | Compute consensus edges for a tree under some criterion |
| contMap | Map continuous trait evolution on the tree |
| cophylo | Creates a co-phylogenetic plot |
| cordylid.data | Phylogenetic datasets |
| cordylid.tree | Phylogenetic datasets |
| cospeciation | Conducts a statistical test of cospeciation between two trees |
| cotangleplot | Creates a co-phylogenetic plot |
| countSimmap | Counts the number of character changes on a object of class '"simmap"' or '"multiSimmap"' |
| ctt | Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories |
-- D --
| darter.tree | Phylogenetic datasets |
| density.anc.Bayes | Bayesian ancestral character estimation |
| density.mcmcMk | Fits extended M_k_ model for discrete character evolution |
| density.multiSimmap | Computes a posterior distribution for the number and types of changes on the tree |
| densityMap | Plot posterior density of stochastic mapping on a tree |
| densityTree | Plots a posterior sample of trees |
| describe.simmap | Summarizes a stochastic mapped tree or set of trees |
| di2multi.contMap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| di2multi.densityMap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| di2multi.multiSimmap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| di2multi.simmap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| dot.legend | Creates a phylogenetic dot plot |
| dotTree | Creates a phylogenetic dot plot |
| drop.clade | Drop a clade from a tree |
| drop.leaves | Drop all the leaves (tips) from a tree |
| drop.tip.contMap | Drop tip or tips from an object of class '"contMap"' or '"densityMap"' |
| drop.tip.densityMap | Drop tip or tips from an object of class '"contMap"' or '"densityMap"' |
| drop.tip.multiSimmap | Drop or keep tip or tips from an object of class '"multiSimmap"' |
| drop.tip.simmap | Drop tips or extract clade from tree with mapped discrete character |
| drop.tip.singleton | Converts a tree without singletons to a tree with singleton nodes |
| Dtest | Conducts correlational D-test from stochastic mapping |
-- E --
| edge.widthMap | Map continuous trait evolution on the tree |
| edgelabels.cophylo | Add labels to a plotted "cophylo" object |
| edgeProbs | Compute the relative frequencies of state changes along edges |
| eel.data | Phylogenetic datasets |
| eel.tree | Phylogenetic datasets |
| elapidae.tree | Phylogenetic datasets |
| errorbar.contMap | Map continuous trait evolution on the tree |
| estDiversity | Estimate diversity at each node of the tree |
| evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| evol.vcv | Likelihood test for variation in the evolutionary variance-covariance matrix |
| evolvcv.lite | Likelihood test for a shift in the evolutionary correlation between traits |
| exhaustiveMP | Exhaustive and branch & bound MP optimization |
| expand.clade | Expands (or contracts) the tip-spacing of a given clade or clades |
| export.as.xml | Export trees & data in XML format |
| extract.clade.simmap | Drop tips or extract clade from tree with mapped discrete character |
| extract.strahlerNumber | Computes Strahler number for trees and nodes |
-- F --
| fancyTree | Plots special types of phylogenetic trees |
| fastAnc | (Reasonably) fast estimation of ML ancestral states |
| fastBM | (Reasonably) fast quantitative trait simulation on phylogenies |
| fastDist | Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa |
| fastHeight | Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa |
| fastMRCA | Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa |
| findMRCA | Get the MRCA of a set of taxa |
| fit.bd | Fits birth-death (speciation/extinction) model to reconstructed phylogeny |
| fit.yule | Fits birth-death (speciation/extinction) model to reconstructed phylogeny |
| fitBayes | Evolutionary model fitting with intraspecific variability using Bayesian MCMC |
| fitDiversityModel | Fit diversity-dependent phenotypic evolution model |
| fitgammaMk | Fits extended M_k_ model for discrete character evolution |
| fitHRM | Fits extended M_k_ model for discrete character evolution |
| fitMk | Fits extended M_k_ model for discrete character evolution |
| fitMk.parallel | Fits extended M_k_ model for discrete character evolution |
| fitmultiMk | Fits extended M_k_ model for discrete character evolution |
| fitPagel | Function to test for correlated evolution of binary traits |
| fitpolyMk | Fits extended M_k_ model for discrete character evolution |
| flatworm.data | Phylogenetic datasets |
| flatworm.tree | Phylogenetic datasets |
| force.ultrametric | Coerces a phylogenetic tree to be ultrametric |
-- G --
| gammatest | Gamma test of Pybus & Harvey (2000) |
| gamma_pruning | Internally used function |
| genSeq | Simulate a DNA alignment on the tree under a model |
| genus.to.species.tree | Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree |
| geo.legend | Adds a geological (or other temporal) legend to a plotted tree |
| geo.palette | Adds a geological (or other temporal) legend to a plotted tree |
| get.treepos | Get position or node of a plotted tree interactively |
| getCladesofSize | Get all subtrees larger than or equal to a specified size |
| getDescendants | Get descendant node numbers |
| getExtant | Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips |
| getExtinct | Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips |
| getnode | Get position or node of a plotted tree interactively |
| getParent | Get descendant node numbers |
| getSisters | Get the sister node number, label, or set of nodes for a node or tip |
| getStates | Get the states at nodes or tips from a mapped tree |
| graph.polyMk | Fits extended M_k_ model for discrete character evolution |
| gtt | Creates lineage-through-time plot (including extinct lineages) |
-- H --
| hide.hidden | Compute marginal or joint ancestral state estimates |
-- K --
| keep.tip.contMap | Drop tip or tips from an object of class '"contMap"' or '"densityMap"' |
| keep.tip.densityMap | Drop tip or tips from an object of class '"contMap"' or '"densityMap"' |
| keep.tip.multiSimmap | Drop or keep tip or tips from an object of class '"multiSimmap"' |
| keep.tip.simmap | Drop tips or extract clade from tree with mapped discrete character |
-- L --
| labelnodes | Function to interactively label nodes of a plotted tree |
| ladderize.simmap | Ladderize a tree with a mapped discrete character |
| lambda.transform | lambda transformation of matrix |
| lik.bd | Fits birth-death (speciation/extinction) model to reconstructed phylogeny |
| likMlambda | Likelihood for joint lambda |
| likSurface.rateshift | Find the temporal position of one or more rate shifts |
| linklabels | Function to add tip labels to a plotted tree with linking lines |
| liolaemid.data | Phylogenetic datasets |
| liolaemid.tree | Phylogenetic datasets |
| locate.fossil | Locate a fossil lineage in a tree using continuous characters |
| locate.yeti | Locate a cryptic, recently extinct, or missing taxon on a tree |
| logLik.fitDiversityModel | Fit diversity-dependent phenotypic evolution model |
| ls.consensus | Compute an average tree from a set of trees and related operations |
| ls.tree | Least squares branch lengths for a given tree |
| ltt | Creates lineage-through-time plot (including extinct lineages) |
| ltt.multiPhylo | Creates lineage-through-time plot (including extinct lineages) |
| ltt.multiSimmap | Creates lineage-through-time plot (including extinct lineages) |
| ltt.phylo | Creates lineage-through-time plot (including extinct lineages) |
| ltt.simmap | Creates lineage-through-time plot (including extinct lineages) |
| ltt95 | Creates a (1-alpha)% CI for a set of LTTs |
-- M --
| make.era.map | Create "era" map on a phylogenetic tree |
| make.simmap | Simulate stochastic character maps on a phylogenetic tree or trees |
| make.transparent | Plots a posterior sample of trees |
| mammal.data | Phylogenetic datasets |
| mammal.geog | Phylogenetic datasets |
| mammal.tree | Phylogenetic datasets |
| Map.Overlap | Proportional overlap between two mapped character histories on a tree |
| map.overlap | Proportional overlap between two mapped character histories on a tree |
| map.to.singleton | Converts a tree without singletons to a tree with singleton nodes |
| mapped.states | Returns a vector, matrix, or list of the mapped states on a tree or set of trees |
| markChanges | Add marked changes to a plotted tree with mapped discrete character |
| matchLabels | Matches nodes between two trees |
| matchNodes | Matches nodes between two trees |
| mccr | Creates lineage-through-time plot (including extinct lineages) |
| mcmcMk | Fits extended M_k_ model for discrete character evolution |
| mergeMappedStates | Merge two or more mapped states into one state |
| midpoint.root | Midpoint root a phylogeny |
| midpoint_root | Midpoint root a phylogeny |
| minRotate | Rotates all nodes of the tree to minimize the difference in order with a vector |
| minSplit | Finding the minimum (median) split in the posterior sample |
| minTreeDist | Compute an average tree from a set of trees and related operations |
| modified.Grafen | Computes modified Grafen edge lengths |
| mrp.supertree | Matrix representation parsimony supertree estimation |
| multi.mantel | Multiple matrix regression (partial Mantel test) |
| multi2di.contMap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| multi2di.densityMap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| multi2di.multiSimmap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| multi2di.simmap | Collapse or resolve polytomies in a tree with a character painted on the edges |
| multiC | Returns a list with phylogenetic VCV matrix for each mapped state |
| multiOU | Brownian or OU simulation with multiple evolutionary regimes |
| multirateBM | Function to fit a multi-rate Brownian evolution model |
| multiRF | Computes Robinson-Foulds distance between a set of trees |
-- N --
| node.paths | Computes modified Grafen edge lengths |
| nodeheight | Compute the heights above the root of each node |
| nodeHeights | Compute the heights above the root of each node |
| nodelabels.cophylo | Add labels to a plotted "cophylo" object |
-- O --
| optim.phylo.ls | Phylogeny inference using the least squares method |
| orderMappedEdge | Order the columns of mapped.edge to match across trees |
-- P --
| paintBranches | Paint sub-trees with a discrete character |
| paintSubTree | Paint sub-trees with a discrete character |
| paste.tree | Paste two trees together |
| pbtree | Simulate pure-birth or birth-death stochastic tree or trees |
| pgls.Ives | Phylogenetic regression with intraspecific sampling error |
| pgls.SEy | Phylogenetic regression with intraspecific sampling error |
| phenogram | Plot traitgram (phenogram) |
| phenogram95 | Plots special types of phylogenetic trees |
| phyl.cca | Phylogenetic canonical correlation analysis |
| phyl.pairedttest | Phylogenetic paired _t_-test |
| phyl.pca | Phylogenetic principal components analysis |
| phyl.resid | Phylogenetic size-correction via GLS regression |
| phyl.RMA | Phylogenetic reduced major axis (RMA) regression |
| phyl.vcv | Compute evolutionary VCV matrix for a tree & dataset |
| phylANOVA | Phylogenetic ANOVA and post-hoc tests |
| phylo.heatmap | Creates a phylogenetic heat map |
| phylo.impute | Phylogenetic imputation for multivariate continuous character data |
| phylo.to.map | Plot tree with tips linked to geographic coordinates |
| phylo.toBackbone | Converts tree to backbone or vice versa |
| phyloDesign | Compute design matrix for least squares analyses |
| phylomorphospace | Creates phylomorphospace plot |
| phylomorphospace3d | Creates three-dimensional phylomorphospace plot |
| phyloScattergram | Plots special types of phylogenetic trees |
| phylosig | Compute phylogenetic signal with two methods |
| phytools | phytools: Phylogenetic Tools for comparative biology (and other things) |
| plot.anc.Bayes | Bayesian ancestral character estimation |
| plot.ancr | Compute marginal or joint ancestral state estimates |
| plot.backbonePhylo | Plots backbone tree with triangles as clades |
| plot.changesMap | Computes a posterior distribution for the number and types of changes on the tree |
| plot.contMap | Map continuous trait evolution on the tree |
| plot.cophylo | Creates a co-phylogenetic plot |
| plot.cospeciation | Conducts a statistical test of cospeciation between two trees |
| plot.density.mcmcMk | Fits extended M_k_ model for discrete character evolution |
| plot.densityMap | Plot posterior density of stochastic mapping on a tree |
| plot.describe.simmap | Summarizes a stochastic mapped tree or set of trees |
| plot.edge.widthMap | Map continuous trait evolution on the tree |
| plot.expand.clade | Expands (or contracts) the tip-spacing of a given clade or clades |
| plot.fitHRM | Fits extended M_k_ model for discrete character evolution |
| plot.fitMk | Fits extended M_k_ model for discrete character evolution |
| plot.fitPagel | Function to test for correlated evolution of binary traits |
| plot.fitpolyMk | Fits extended M_k_ model for discrete character evolution |
| plot.gfit | Fits extended M_k_ model for discrete character evolution |
| plot.ltt95 | Creates a (1-alpha)% CI for a set of LTTs |
| plot.mcmcMk | Fits extended M_k_ model for discrete character evolution |
| plot.multiSimmap | Plot stochastic character mapped tree |
| plot.phyl.RMA | Phylogenetic reduced major axis (RMA) regression |
| plot.phylo.to.map | Plot tree with tips linked to geographic coordinates |
| plot.phylosig | Compute phylogenetic signal with two methods |
| plot.Qmatrix | Convert a fitted M_k_ model to a Q-matrix |
| plot.rateshift | Find the temporal position of one or more rate shifts |
| plot.simBMphylo | Creates a graphical illustration of Brownian motion evolution on a phylogeny |
| plot.simmap | Plot stochastic character mapped tree |
| plot.summary.evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| plotBranchbyTrait | Plot branch colors by a quantitative trait or value |
| plotSimmap | Plot stochastic character mapped tree |
| plotThresh | Tree plotting with posterior probabilities of ancestral states from the threshold model |
| plotTree | Plots rooted phylogenetic tree |
| plotTree.barplot | Plot a tree with bars at the tips |
| plotTree.boxplot | Plot a tree with bars at the tips |
| plotTree.datamatrix | Plot a tree with a discrete character data matrix at the tips |
| plotTree.errorbars | Plot a tree with error bars around divergence dates |
| plotTree.singletons | Converts a tree without singletons to a tree with singleton nodes |
| plotTree.splits | Plots a phylogeny in two columns |
| plotTree.wBars | Plot a tree with bars at the tips |
| posterior.evolrate | Analysis of the posterior sample from evol.rate.mcmc |
| posthoc | Generic post-hoc test |
| posthoc.ratebytree | Likelihood test for rate variation among trees, clades, or traits |
| primate.data | Phylogenetic datasets |
| primate.tree | Phylogenetic datasets |
| print.backbonePhylo | Print method for backbone phylogeny |
| print.cospeciation | Conducts a statistical test of cospeciation between two trees |
| print.evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| print.fit.bd | Fits birth-death (speciation/extinction) model to reconstructed phylogeny |
| print.fitDiversityModel | Fit diversity-dependent phenotypic evolution model |
| print.Qmatrix | Convert a fitted M_k_ model to a Q-matrix |
| print.summary.evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| project.phylomorphospace | Creates phylomorphospace plot |
| pscore | Compute the parsimony score |
-- R --
| ratebystate | Method for investigating the rate of one trait as a function of the state of another |
| ratebytree | Likelihood test for rate variation among trees, clades, or traits |
| rateshift | Find the temporal position of one or more rate shifts |
| read.newick | Newick or Nexus style tree reader |
| read.simmap | Read SIMMAP style trees from file |
| readNexus | Newick or Nexus style tree reader |
| reorder.backbonePhylo | Reorders a backbone phylogeny |
| reorderSimmap | Reorder edges of a '"simmap"' tree |
| rep.multiPhylo | Replicate a tree or set of trees |
| rep.phylo | Replicate a tree or set of trees |
| repPhylo | Replicate a tree or set of trees |
| reroot | Re-root a tree along an edge |
| rerootingMethod | Get marginal ancestral state reconstructions by re-rooting |
| rescale | Rescale phylogenetic objects of different types |
| rescale.multiSimmap | Rescale object of class '"simmap"' |
| rescale.simmap | Rescale object of class '"simmap"' |
| rescaleSimmap | Rescale object of class '"simmap"' |
| resolveAllNodes | Compute all possible resolutions of a node or all nodes in a multifurcating tree |
| resolveNode | Compute all possible resolutions of a node or all nodes in a multifurcating tree |
| rootedge.to.singleton | Converts a tree without singletons to a tree with singleton nodes |
| rotate.multi | Rotates a node or set of nodes in a phylogenetic tree |
| rotateNodes | Rotates a node or set of nodes in a phylogenetic tree |
| roundBranches | Rounds the branch lengths of a tree |
| roundPhylogram | Plot a round, sigmoidal, or spline phylogram or cladogram |
| rstate | Pick a random state according to a vector of probabilities |
-- S --
| salamanders | Phylogenetic datasets |
| sampleFrom | Sample from a set of distributions |
| scores | Phylogenetic principal components analysis |
| scores.phyl.pca | Phylogenetic principal components analysis |
| setMap | Set color map for various phylogenetic objects of classes |
| setMap.contMap | Set color map for various phylogenetic objects of classes |
| setMap.densityMap | Set color map for various phylogenetic objects of classes |
| setMap.multirateBM_plot | Set color map for various phylogenetic objects of classes |
| setMap.phyloScattergram | Set color map for various phylogenetic objects of classes |
| sigmoidPhylogram | Plot a round, sigmoidal, or spline phylogram or cladogram |
| sim.corrs | Multivariate Brownian simulation with multiple correlations and rates |
| sim.ctt | Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories |
| sim.history | Simulate character history or a discrete character at the tips of the tree under some model |
| sim.Mk | Simulate character history or a discrete character at the tips of the tree under some model |
| sim.multiCtt | Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories |
| sim.multiMk | Simulate character history or a discrete character at the tips of the tree under some model |
| sim.ratebystate | Conduct simulation of state dependent rate variation |
| sim.rates | Brownian or OU simulation with multiple evolutionary regimes |
| simBMphylo | Creates a graphical illustration of Brownian motion evolution on a phylogeny |
| simmap | Simulate stochastic character maps on a phylogenetic tree or trees |
| skewers | Matrix comparison using the method of random skewers |
| splinePhylogram | Plot a round, sigmoidal, or spline phylogram or cladogram |
| splitEdgeColor | Split edge colors when descendant edges have different mapped states |
| splitplotTree | Plots a phylogeny in two columns |
| splitTree | Split tree at a point |
| starTree | Create star phylogeny |
| strahlerNumber | Computes Strahler number for trees and nodes |
| summary.evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| summary.multiSimmap | Summarizes a stochastic mapped tree or set of trees |
| summary.simmap | Summarizes a stochastic mapped tree or set of trees |
| sunfish.data | Phylogenetic datasets |
| sunfish.tree | Phylogenetic datasets |
-- T --
| threshBayes | Threshold model using Bayesian MCMC |
| threshDIC | Deviance Information Criterion from the threshold model |
| threshState | Computes value for a threshold character from a liability and thresholds |
| tiplabels.cophylo | Add labels to a plotted "cophylo" object |
| tipRotate | Rotates all nodes of the tree to minimize the difference in order with a vector |
| to.matrix | Convert a character vector to a binary matrix |
| tortoise.geog | Phylogenetic datasets |
| tortoise.tree | Phylogenetic datasets |
| tree.grow | Creates an animation of a tree growing from left-to-right or upwards |
| treeSlice | Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point |
| tropidurid.data | Phylogenetic datasets |
| tropidurid.tree | Phylogenetic datasets |
-- U --
| untangle | Attempts to untangle crossing branches for plotting |
-- V --
| vcvPhylo | Calculates cophenetic (i.e., phylogenetic VCV) matrix |
| vertebrate.data | Phylogenetic datasets |
| vertebrate.tree | Phylogenetic datasets |
-- W --
| wasp.data | Phylogenetic datasets |
| wasp.trees | Phylogenetic datasets |
| whale.tree | Phylogenetic datasets |
| write.simmap | Write a stochastic character mapped tree to file |
| writeAncestors | Write a tree to file with ancestral states and (optionally) CIs at nodes |
| writeNexus | Write a tree to file in Nexus format |