API for ms609/TreeSearch
Phylogenetic Tree Search Using Custom Optimality Criteria

Global functions
AddTip Man page Source code
AllAncestors Man page Source code
AllDescendantEdges Man page Source code
AllSPR Man page Source code
AllTBR Man page Source code
AncestorEdge Man page Source code
ApeTime Man page Source code
AsBinary Man page Source code
Assert Source code
C_MorphyLength Man page Source code
C_node_depth Man page Source code
CladeSizes Man page Source code
Cladewise Man page Source code
CollapseEdge Man page Source code
CollapseNode Man page Source code
ConsensusWithout Man page Source code
DFact Man page
DescendantEdges Man page Source code
DoubleFactorial Man page Source code
DoubleNNI Man page Source code
DropSingleSplits Man page Source code
EdgeAncestry Man page Source code
EdgeListSearch Man page Source code
EnforceOutgroup Man page Source code
Evaluate Man page Source code
ExtractTaxa Man page Source code
FastTable Source code
Fitch Man page Source code
FitchSteps Man page Source code
ForestSplits Man page Source code
GetMorphyLength Man page Source code
IC1Spr Man page Source code
ICPerStep Man page Source code
ICS Man page
ICSteps Man page Source code
IWBootstrap Man page Source code
IWDestroyMorphy Man page
IWInitMorphy Man page Source code
IWMultiRatchet Man page Source code
IWRatchet Man page Source code
IWRatchetConsensus Man page
IWScore Man page Source code
IWScoreMorphy Man page Source code
IWTreeSearch Man page Source code
InfoAmounts Man page Source code
Jackknife Man page Source code
LDFact Man page
LDFactorial Man page
ListToMatrix Man page Source code
LnRooted Man page
LnUnrooted Man page Source code
LnUnrooted1 Man page
LnUnrootedMult Man page Source code
Lobo.data Man page
Lobo.phy Man page
LogisticPoints Man page Source code
MarkMissing Man page Source code
MatrixToList Man page Source code
MatrixToPhyDat Man page Source code
MinimumSteps Man page Source code
MorphyBootstrap Man page Source code
MorphyErrorCheck Man page Source code
MorphyLength Man page Source code
MorphyTreeLength Man page Source code
MorphyWeights Man page Source code
MultiRatchet Man page Source code
N1Spr Man page Source code
NJTree Man page Source code
NNI Man page Source code
NNISwap Man page Source code
NRooted Man page
NUnrooted Man page Source code
NUnrooted1 Man page
NUnrootedMult Man page Source code
NamedConstant Man page Source code
NewickTree Man page Source code
NeworderPhylo Man page Source code
NeworderPruningwise Man page Source code
NonDuplicateRoot Man page Source code
OrderEdgesNumberNodes Man page Source code
PhyDat Man page Source code
PhyDat2Morphy Man page Source code
PhyToString Man page Source code
Postorder Man page Source code
PostorderEdges Man page Source code
Preorder Man page Source code
PrepareDataIW Man page Source code
PrepareDataProfile Man page Source code
PrepareDataSA Source code
ProfileBootstrap Man page Source code
ProfileDestroyMorphy Man page Source code
ProfileInitMorphy Man page Source code
ProfileRatchet Man page Source code
ProfileScore Man page Source code
ProfileScoreMorphy Man page Source code
ProfileTreeSearch Man page Source code
Pruningwise Man page Source code
RandomMorphyTree Man page Source code
RandomTree Man page Source code
RandomTreeScore Man page Source code
Ratchet Man page Source code
RatchetConsensus Man page
ReadAsPhyDat Man page Source code
ReadCharacters Man page Source code
ReadTntAsPhyDat Man page Source code
ReadTntCharacters Man page Source code
ReadTntTree Man page Source code
RearrangeEdges Man page Source code
Renumber Man page Source code
RenumberEdges Man page Source code
RenumberTips Man page Source code
RenumberTree Man page Source code
RightmostCharacter Man page Source code
RootTree Man page Source code
RootedNNI Man page Source code
RootedNNISwap Man page Source code
RootedSPR Man page Source code
RootedSPRSwap Man page Source code
RootedTBR Man page Source code
RootedTBRSwap Man page Source code
SPR Man page Source code
SPRSwap Man page Source code
SPRWarning Man page Source code
SampleOne Man page Source code
SetMorphyWeights Man page Source code
SingleCharMorphy Man page Source code
SingleTaxonTree Man page Source code
SortTree Man page Source code
SplitFrequency Man page Source code
SplitNumber Man page Source code
SplitsRepeated Man page Source code
StringToPhyDat Man page
StringToPhydat Man page
Suboptimality Man page Source code
Subtree Man page Source code
SuccessiveApproximations Man page Source code
SuccessiveWeights Man page Source code
SupportColor Man page
SupportColour Man page Source code
TBR Man page Source code
TBRMoves Man page Source code
TBRSwap Man page Source code
TBRWarning Man page Source code
TNTText2Tree Man page Source code
TipsAreColumns Man page Source code
TipsAreNames Man page Source code
Tree2Bipartitions Man page
Tree2Splits Man page Source code
TreeSearch Man page Source code
TreeSplits Man page Source code
UniqueExceptHits Man page Source code
UniqueSplits Man page Source code
UnloadMorphy Man page Source code
UnloadTreeSearch Man page Source code
WithOneExtraStep Man page Source code
brewer Man page
congreveLamsdellMatrices Man page
inapplicable.citations Man page
inapplicable.datasets Man page
inapplicable.phyData Man page
mpl_apply_tipdata Man page Source code
mpl_attach_rawdata Man page Source code
mpl_attach_symbols Man page Source code
mpl_delete_Morphy Man page Source code
mpl_delete_rawdata Man page Source code
mpl_first_down_recon Man page Source code
mpl_first_up_recon Man page Source code
mpl_get_charac_weight Man page Source code
mpl_get_num_charac Man page Source code
mpl_get_num_internal_nodes Man page Source code
mpl_get_numtaxa Man page Source code
mpl_get_symbols Man page Source code
mpl_init_Morphy Man page Source code
mpl_new_Morphy Man page Source code
mpl_second_down_recon Man page Source code
mpl_second_up_recon Man page Source code
mpl_set_charac_weight Man page Source code
mpl_set_num_internal_nodes Man page Source code
mpl_set_parsim_t Man page Source code
mpl_translate_error Man page Source code
mpl_update_lower_root Man page Source code
mpl_update_tip Man page Source code
phangorn_bipCPP Source code
plot.morphyTree Source code
referenceTree Man page
release_questions Source code Source code
summary.morphyPtr Man page Source code
ms609/TreeSearch documentation built on Dec. 8, 2018, 4:23 p.m.