dist.dna, new2old.phylo, cophenetic.phylo, is.rooted, unroot, root,
is.binary, as.alignment, di2multi, multi2di, .uncompressTipLabel,
.compressTipLabel, prop.part, Ntip, getMRCA, postprocess.prop.part,
speciesTree, plotPhyloCoor, cladogram.plot, phylogram.plot, has.singles,
node.depth.edgelength, drop.tip, stree, rtree, rcoal, rmtree,
is.ultrametric, .PlotPhyloEnv, nodelabels, edgelabels, BOTHlabels,
read.nexus.data, write.nexus.data, read.dna, write.dna, reorder.phylo,
dist.nodes, collapse.singles, rotate, prop.clades, fastme.bal, fastme.ols,
Nnode, image.DNAbin, ONEwise, as.AAbin, as.phyDat.AAbin, image.AAbin,
plot.igraph, shortest_paths, set.edge.attribute, set_edge_attr, decompose,
components, groups, vcount, graph.edgelist, graph_from_edgelist, topo_sort,
importFrom(stats, AIC, BIC, logLik, reorder, update, optim, optimize,
constrOptim, na.omit, cophenetic, hclust, as.dist, pchisq, reshape, qgamma,
pgamma, model.matrix, aggregate, lm.fit, xtabs, quantile, sd, runif)
importFrom(graphics, plot, plot.default, plot.new, plot.window, text, par,
abline, strwidth, axis, title, segments, points, image, matplot, legend,
export(pml, optim.pml, pml.control, parsimony, optim.parsimony, pratchet, NJ,
UNJ, PNJ, phyDat, cbind.phyDat, read.phyDat, write.phyDat, as.Matrix,
as.phyDat, as.splits, as.networx, dfactorial, ldfactorial, hadamard, nni,
allSitePattern, allSplits, allCircularSplits, fhm, distanceHadamard,
treedist, sankoff, fitch, h2st, h4st, dist.logDet, dist.hamming,
dist.ml, dist.p, unique.dist, upgma, wpgma, write.nexus.splits,
write.nexus.dist, pmlPart, pmlCluster, pmlMix, pmlPen, read.aa, allTrees,
designTree, designSplits, nnls.tree, nnls.splits, nnls.phylo, nnls.networx,
neighborNet, pmlPart2multiPhylo, multiphyDat2pmlPart, splitsNetwork, simSeq,
SH.test, bootstrap.pml, bootstrap.phyDat, RF.dist, wRF.dist, KF.dist,
path.dist, sprdist, SPR.dist, mast, rNNI, rSPR, plotBS, Ancestors,
Descendants, allDescendants, mrca.phylo, Children, Siblings, pace,
modelTest, lento, compatible, acgt2ry, ancestral.pars, ancestral.pml, CI,
RI, getClans, getSlices, getClips, getDiversity, midpoint, pruneTree,
acctran, getRoot, plotAnc, consensusNet, bab, random.addition, diversity,
baseFreq, densiTree, superTree, coalSpeciesTree, pml.fit, pml.init,
pml.free, edQt, lli, cladePar, addConfidences, createLabel, SOWH.test,