Node-class              Node-class
TreeMan-class           TreeMan-class
TreeMan-to-phylo        Convert TreeMan to phylo
TreeMen-class           TreeMen-class
TreeMen-to-multiPhylo   Convert TreeMen to multiPhylo
addClade                Add clade to tree
addNdmtrx               Add node matrix to a tree
addTip                  Add tip to a tree
birds                   Phylogenetic tree of Aves
blncdTree               Generate a balanced tree
cTrees                  cTrees
calcDstBLD              Calculate the BLD between two trees
calcDstMtrx             Calculate the distance matrix
calcDstRF               Calculate the Robinson-Foulds distance between
                        two trees
calcDstTrp              Calculate the triplet distance between two
                        trees
calcFrPrp               Calculate evolutionary distinctness
calcNdBlnc              Calculate the balance of a node
calcNdsBlnc             Calculate the balances of all nodes
calcOvrlp               Calculate phylogenetic overlap
calcPhyDv               Calculate phylogenetic diversity
calcPrtFrPrp            Calculate evolutionary distinctness for part of
                        tree
checkNdlst              Check if ndlst is correct
checkTreeMen            Check if trees are correct
fastCheckTreeMan        Check if tree is correct, fast!
getAge                  Get age of tree
getBiprts               Get the sets of labels for each bipartition in
                        tree
getCnnctdNds            Get all nodes connected by given tips
getDcsd                 Get extinct tips from a tree
getLvng                 Get extant tips from a tree
getNdAge                Get age
getNdKids               Get children IDs
getNdLng                Get lineage
getNdPD                 Get phylogenetic diversity of node
getNdPrdst              Get pre-distance
getNdPrids              Get pre-nodes to root
getNdPtids              Get post-nodes to tips
getNdSlt                Get a node slot
getNdSstr               Get sister id
getNdsAge               Get ages for multiple nodes
getNdsFrmTxnyms         Get IDs for nodes represented txnyms
getNdsKids              Get children IDs for multiple nodes
getNdsLng               Get lineage for multiple nodes
getNdsPD                Get phylogenetic diversities of nodes
getNdsPrdst             Get pre-distances
getNdsPrids             Get pre-nodes for multiple nodes
getNdsPtids             Get post-nodes to tips for multiple nodes
getNdsSlt               Get a node slot for multiple nodes
getNdsSstr              Get sister id
getOtgrp                Get outgroup
getPath                 Get path between nodes
getPrnt                 Get parent
getSpnAge               Get age range
getSpnsAge              Get age ranges for multiple nodes
getSubtree              Get subtree
getUnqNds               Get unique nodes represented by tips
isUltrmtrc              Is tree ultrametric?
list-to-TreeMen         Convert list to a TreeMen
loadTreeMan             Load a TreeMan object in serialization format
mammals                 Phylogenetic tree of Mammalia
multiPhylo-class        multiPhylo class
multiPhylo-to-TreeMen   Convert multiPhylo to TreeMen
phylo-class             phylo class
phylo-to-TreeMan        Convert phylo to TreeMan
pinTips                 Pin tips to a tree
plants                  Phylogenetic tree of European Flora
pstMnp                  Update prinds and tinds
randTree                Generate a random tree
readTree                Read a Newick tree
readTrmn                Read a .trmn tree
rmClade                 Remove a clade from a tree
rmNdmtrx                Remove node matrix
rmNodes                 Remove nodes from a tree
rmOtherSlt              Remove a user-defined slot
rmTips                  Remove tips from a tree
saveTreeMan             Save a TreeMan object in serialization format
searchTxnyms            Get node labels based on online taxonomic
                        database
setAge                  Set the age of a tree
setNdID                 Set the ID of a node
setNdOther              Set a user defined slot
setNdSpn                Set the branch length of a specific node
setNdsID                Set the IDs of multiple nodes
setNdsOther             Set a user defined slot for multiple nodes
setNdsSpn               Set the branch lengths of specific nodes
setPD                   Set the phylogenetic diversity
setTxnyms               Set the txnym slots in a tree
taxaResolve             Resolve taxonmic names online
treeman-package         Phylogenetic Tree Manipulation
twoer                   Generate a tree of two tips
ultrTree                Make tree ultrametric
unblncdTree             Generate an unbalanced tree
updateSlts              Update tree slots after manipulation
writeTree               Write a Newick tree
writeTrmn               Write a .trmn tree
