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 |
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 |
cTrees | cTrees |
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 |
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 |
getNdSlt | Get a node slot |
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 |
getNdSstr | 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 |
Node-class | Node-class |
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 |
setNdsID | Set the IDs of multiple nodes |
setNdsOther | Set a user defined slot for multiple nodes |
setNdSpn | Set the branch length of a specific node |
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-class | TreeMan-class |
treeman-package | Phylogenetic Tree Manipulation |
TreeMan-to-phylo | Convert TreeMan to phylo |
TreeMen-class | TreeMen-class |
TreeMen-to-multiPhylo | Convert TreeMen to multiPhylo |
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 |
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