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 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
ConsensusWithout Source code
DescendantEdges Man page Source code
DoubleFactorial Source code
DoubleNNI Man page Source code
EdgeAncestry Man page Source code
EdgeListSearch Man page Source code
EnforceOutgroup Man page Source code
Evaluate Source code
ExtractTaxa Source code
FastTable Source code
Fitch Man page Source code
FitchSteps Source code
ForestSplits Source code
GetMorphyLength Man page Source code
IC1Spr Source code
ICPerStep Source code
ICSteps Source code
IWBootstrap Man page Source code
IWInitMorphy Source code
IWMultiRatchet Man page Source code
IWRatchet Man page Source code
IWRatchetConsensus Man page
IWScore Source code
IWScoreMorphy Source code
IWTreeSearch Man page Source code
InfoAmounts Source code
Jackknife Man page Source code
ListToMatrix Man page Source code
LnUnrooted Source code
LnUnrootedMult Source code
Lobo.data Man page
Lobo.phy Man page
LogisticPoints Source code
MarkMissing Source code
MatrixToList Man page Source code
MatrixToPhyDat Source code
MinimumSteps 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 Source code
NJTree Man page Source code
NNI Man page Source code
NNISwap Man page Source code
NUnrooted Source code
NUnrootedMult Source code
NamedConstant Source code
NewickTree Source code
NeworderPhylo Man page Source code
NeworderPruningwise Man page Source code
NonDuplicateRoot Source code
OrderEdgesNumberNodes Man page Source code
PhyDat 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 Source code
PrepareDataProfile Source code
PrepareDataSA Source code
ProfileBootstrap Man page Source code
ProfileDestroyMorphy Source code
ProfileInitMorphy Source code
ProfileRatchet Man page Source code
ProfileScore Source code
ProfileScoreMorphy 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 Source code
ReadCharacters Source code
ReadTntAsPhyDat Source code
ReadTntCharacters Source code
ReadTntTree Source code
RearrangeEdges Source code
Renumber Man page Source code
RenumberEdges Man page Source code
RenumberTips Man page Source code
RenumberTree Man page Source code
RightmostCharacter Source code
RootTree 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 Source code
SplitFrequency Source code
SplitNumber 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
SupportColour Source code
TBR Man page Source code
TBRMoves Man page Source code
TBRSwap Man page Source code
TBRWarning Man page Source code
TNTText2Tree Source code
TipsAreColumns Man page Source code
TipsAreNames Man page Source code
TreeSearch Man page Source code
TreeSplits Source code
UniqueExceptHits Source code
UnloadMorphy Man page Source code
UnloadTreeSearch Source code
WithOneExtraStep Source code
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
plot.morphyTree Source code
release_questions Source code
summary.morphyPtr Man page Source code
ms609/TreeSearch documentation built on Sept. 22, 2018, 7:35 p.m.