pmlPart, pmlCluster, pmlMix, pmlPen, read.aa, allTrees,

dfactorial, ldfactorial, hadamard, nni, allSitePattern,
designTree, designSplits, splitsNetwork, simSeq, SH.test, bootstrap.pml,

bootstrap.phyDat, RF.dist, pmlCluster2, rNNI, rSPR)

bootstrap.phyDat, RF.dist, rNNI, rSPR, plotBS, Ancestors, Descendants,

phyDat, read.phyDat, write.phyDat, as.phyDat, as.splits,
Children, Siblings, pace, modelTest, lento)

dist.logDet, dist.hamming, dist.ml, upgma, wpgma, write.nexus.splits,
Children, Siblings, pace, modelTest, lento, compatible, acgt2ry,

export(pml, optim.pml, pml.control, parsimony, optim.parsimony, NJ, UNJ, PNJ,

ancestral.pars, ancestral.pml, CI, RI, getClans, getSlices, getClips, getDiversity)
#    optim.fitch, fitch.nni, fnodes, optim.sankoff)

dist.logDet, dist.hamming, dist.ml, upgma, wpgma, write.nexus.splits, write.splits,

export(pml, optim.pml, pml.control, parsimony, optim.parsimony, pratchet, NJ, UNJ, PNJ,
ancestral.pars, ancestral.pml, CI, RI, getClans, getSlices, getClips, getDiversity,

midpoint, pruneTree, acctran, getRoot, plotAnc)
#    optim.fitch, fitch.nni, fnodes, optim.sankoff, dec2bin, ptree)

phyDat, read.phyDat, write.phyDat, as.phyDat, as.splits, as.prop.part, as.networx,
dfactorial, ldfactorial, hadamard, nni, allSitePattern, allSplits,
midpoint, pruneTree, acctran, getRoot, plotAnc, consensusNet)

designTree, designSplits, nnls.tree, splitsNetwork, simSeq, SH.test, bootstrap.pml,
midpoint, pruneTree, acctran, getRoot, plotAnc, consensusNet, bab, random.addition)
#    optim.fitch, fitch.nni, fnodes, optim.sankoff, dec2bin, ptree, ll3, pmlScale)

midpoint, pruneTree, acctran, getRoot, plotAnc, consensusNet, bab, random.addition, diversity)

midpoint, pruneTree, acctran, getRoot, plotAnc, consensusNet, bab, random.addition, diversity,

bootstrap.phyDat, RF.dist, rNNI, rSPR, plotBS, Ancestors, Descendants, mrca.phylo,

importFrom(igraph, graph, graph.adjacency, layout.kamada.kawai, set.edge.attribute, vcount, as.igraph, edges)
dfactorial, ldfactorial, hadamard, nni, allSitePattern, allSplits, fhm,
distanceHadamard, treedist, sankoff, fitch, h2st, h4st, dist.logDet, dist.hamming,
dist.ml, dist.p, upgma, wpgma, write.nexus.splits, write.splits, pmlPart,
pmlCluster, pmlMix, pmlPen, read.aa, allTrees, designTree, designSplits, nnls.tree,
splitsNetwork, simSeq, SH.test, bootstrap.pml, bootstrap.phyDat, RF.dist, rNNI,
rSPR, plotBS, Ancestors, Descendants, mrca.phylo,