importFrom(ape, as.DNAbin, as.phylo, plot.phylo, as.prop.part, nj,old2new.phylo,
new2old.phylo, is.rooted, unroot, root, is.binary.tree, as.alignment,
di2multi, multi2di, .uncompressTipLabel, .compressTipLabel, prop.part,
postprocess.prop.part, speciesTree, plotPhyloCoor, cladogram.plot, phylogram.plot,
node.depth.edgelength, drop.tip, stree, rtree, is.ultrametric, .PlotPhyloEnv,
nodelabels, edgelabels, BOTHlabels, read.nexus.data, write.nexus.data,
read.dna, write.dna, reorder.phylo, dist.nodes, collapse.singles, rotate)
importFrom(igraph, graph, graph.adjacency, layout.kamada.kawai, plot.igraph,
get.shortest.paths, set.edge.attribute, vcount, graph.edgelist, topological.sort)
importFrom(rgl, open3d, segments3d, spheres3d, rgl.texts)
phyDat, read.phyDat, write.phyDat, as.Matrix, as.phyDat, as.splits, as.networx,
dist.ml, dist.p, upgma, wpgma, write.nexus.splits, read.nexus.splits, write.splits, pmlPart,
rSPR, plotBS, Ancestors, Descendants, 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, countCycles,

importFrom(Matrix, Matrix, sparseMatrix, spMatrix, crossprod, solve)
#importFrom(rgl, open3d, segments3d, spheres3d, rgl.texts)
SOWH.test, plot.networx, presenceAbsence, as.networx.splits, addTrivialSplits)

phyDat, cbind.phyDat, read.phyDat, write.phyDat, as.Matrix, as.phyDat, as.splits, as.networx,
nnls.splits, nnls.phylo, nnls.networx, neighborNet, pmlPart2multiPhylo,

baseFreq, densiTree, superTree, coalSpeciesTree, pml.fit, pml.init, pml.free, edQt, lli)

importFrom(igraph, graph, graph.adjacency, layout.kamada.kawai, set.edge.attribute, vcount, as.igraph)
baseFreq, densiTree, superTree, coalSpeciesTree, pml.fit, pml.init, pml.free, edQt, lli,

importFrom(ape, as.DNAbin, as.phylo, plot.phylo, as.prop.part, nj,old2new.phylo, dist.dna,
new2old.phylo, cophenetic.phylo, is.rooted, unroot, root, is.binary.tree, as.alignment,
importFrom(Matrix, Matrix, sparseMatrix, spMatrix, crossprod, solve) #, %*%
importFrom(stats, AIC, logLik, reorder, update, optim, optimize, constrOptim, na.omit,
cophenetic, hclust, as.dist, pchisq, reshape, qgamma, pgamma, model.matrix,
importFrom(graphics, plot.new, plot.window, text, par, plot, abline, strwidth, axis, title, segments,
importFrom(utils, read.table, download.file, citation, stack, installed.packages, write.table)
SOWH.test, plot.networx, presenceAbsence, as.networx.splits, addTrivialSplits,
phyDat2alignment, AICc, readDist, writeDist, discrete.gamma)