API for TreeSearch
Phylogenetic Analysis with Discrete Character Data
| Global functions | |
|---|---|
| .CombineResults | Man page |
| .ConstraintConstrains | Source code |
| .DateTime | Source code |
| .GapHandler | Man page |
| .NonDuplicateRoot | Man page Source code |
| .PlotCharacter | Source code |
| .Recompress | Source code |
| .ReplaceResults | Man page |
| .Time | Source code |
| .UniqueExceptHits | Man page |
| .vapply | Source code |
| AdditionTree | Man page |
| AllSPR | Man page |
| C_MorphyLength | Man page |
| Carter1 | Man page |
| CharacterLength | Man page |
| ClusterStrings | Man page |
| ClusteringConcordance | Man page |
| ConcordantInfo | Man page |
| ConcordantInformation | Man page |
| Consistency | Man page |
| DoNothing | Man page |
| DoubleNNI | Man page |
| EasyTrees | Man page |
| EasyTreesy | Man page |
| EdgeListSearch | Man page |
| EmptyPhyDat | Man page |
| Evaluate | Man page |
| FastCharacterLength | Man page |
| Fitch | Man page |
| FitchSteps | Man page |
| GapHandler | Man page |
| GetMorphyLength | Man page |
| IWScore | Man page |
| IWTreeSearch | Man page |
| JackLabels | Man page |
| Jackknife | Man page |
| LengthAdded | Man page Source code |
| Log2Carter1 | Man page |
| LogCarter1 | Man page |
| MaximizeParsimony | Man page |
| MaximumLength | Man page Source code |
| MaximumLength.character | Man page |
| MaximumLength.numeric | Man page Source code |
| MinimumLength | Man page |
| MinimumLength.character | Man page |
| MinimumLength.numeric | Man page |
| MinimumLength.phyDat | Man page |
| MinimumSteps | Man page Source code |
| MorphyBootstrap | Man page |
| MorphyErrorCheck | Man page |
| MorphyLength | Man page |
| MorphyTreeLength | Man page |
| MorphyWeights | Man page |
| MultiRatchet | Man page |
| MutualClusteringConcordance | Man page |
| NNI | Man page |
| NNISwap | Man page |
| PhyDat2Morphy | Man page |
| PhylogeneticConcordance | Man page |
| PlotCharacter | Man page Source code |
| PlotCharacter.list | Man page Source code |
| PlotCharacter.multiPhylo | Man page Source code |
| PlotCharacter.phylo | Man page Source code |
| PolEscapa | Man page |
| PrepareDataIW | Man page |
| PrepareDataProfile | Man page |
| QuartetConcordance | Man page |
| QuartetResolution | Man page Source code |
| RandomMorphyTree | Man page |
| RandomTreeScore | Man page |
| Ratchet | Man page |
| RatchetConsensus | Man page |
| RearrangeEdges | Man page |
| Resample | Man page |
| RootedNNI | Man page |
| RootedNNISwap | Man page |
| RootedSPR | Man page Source code |
| RootedSPRSwap | Man page |
| RootedTBR | Man page Source code |
| RootedTBRSwap | Man page |
| SPR | Man page Source code |
| SPRMoves | Man page |
| SPRMoves.matrix | Man page |
| SPRMoves.phylo | Man page |
| SPRSwap | Man page |
| SPRWarning | Man page |
| SetMorphyWeights | Man page |
| SharedPhylogeneticConcordance | Man page |
| SingleCharMorphy | Man page |
| SiteConcordance | Man page |
| StepInformation | Man page |
| StopUnlessBifurcating | Man page |
| Suboptimality | Man page |
| SuccessiveApproximations | Man page |
| SuccessiveWeights | Man page Source code |
| TBR | Man page Source code |
| TBRMoves | Man page |
| TBRMoves.matrix | Man page |
| TBRMoves.phylo | Man page |
| TBRSwap | Man page Source code |
| TBRWarning | Man page |
| TaxonInfluence | Man page Source code |
| TreeLength | Man page |
| TreeLength.list | Man page |
| TreeLength.multiPhylo | Man page |
| TreeLength.numeric | Man page |
| TreeLength.phylo | Man page |
| TreeSearch | Man page |
| UnloadMorphy | Man page |
| WhenFirstHit | Man page Source code |
| WithOneExtraStep | Man page |
| all_spr | Source code |
| all_tbr | Source code |
| cNNI | Man page |
| cSPR | Man page |
| congreveLamsdellMatrices | Man page |
| inapplicable.citations | Man page |
| inapplicable.datasets | Man page |
| inapplicable.phyData | Man page |
| inapplicable.trees | Man page |
| is.morphyPtr | Man page |
| morphy_iw | Source code |
| morphy_profile | Source code |
| 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 |
| mpl_get_gaphandl | Man page |
| 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 |
| mpl_set_gaphandl | Man page |
| mpl_set_num_internal_nodes | Man page Source code |
| mpl_set_parsim_t | Man page Source code |
| mpl_translate_error | Man page |
| mpl_update_lower_root | Man page Source code |
| mpl_update_tip | Man page Source code |
| nni | Source code |
| preorder_morphy | Source code |
| preorder_morphy_by_char | Source code |
| profiles | Man page |
| referenceTree | Man page |
| release_questions | Source code Source code |
| spr | Source code |
| spr_moves | Source code |
| summary.morphyPtr | Man page |
| tbr | Source code |
