Man pages for ms609/TreeSearch
Phylogenetic Analysis with Discrete Character Data
| AdditionTree | Addition tree |
| AllSPR | All SPR trees |
| Carter1 | Number of trees with _m_ steps |
| CharacterLength | Character length |
| ClusterStrings | Cluster similar strings |
| ConcordantInformation | Evaluate the concordance of information between a tree and a... |
| congreveLamsdellMatrices | 100 simulated data matrices |
| Consistency | Consistency / retention "indices" |
| cSPR | 'cSPR()' expects a tree rooted on a single tip. |
| dot-CombineResults | Combine two edge matrices |
| dot-GapHandler | Translate a gap treatment into a string in the format... |
| dot-NonDuplicateRoot | Non-duplicate root |
| dot-UniqueExceptHits | Unique trees (ignoring "hits" attribute) |
| DoubleNNI | Double NNI |
| GapHandler | Read how a Morphy Object handles the inapplicable token |
| inapplicable.datasets | Thirty datasets with inapplicable data |
| is.morphyPtr | Is an object a valid Morphy object? |
| Jackknife | Jackknife resampling |
| JackLabels | Label nodes with jackknife support values |
| LengthAdded | Contribution of character to leaf instability |
| MaximizeParsimony | Find most parsimonious trees |
| MinimumLength | Minimum and Maximum lengths possible for a character |
| MorphyErrorCheck | Check for error whilst modifying Morphy object |
| MorphyTreeLength | Calculate parsimony score from Morphy object |
| MorphyWeights | Set and get the character weightings associated with a Morphy... |
| mpl_apply_tipdata | Commits parameters prior to nodal set calculations. |
| mpl_attach_rawdata | Attach raw character state data (i.e. tip data). |
| mpl_attach_symbols | Attach a caller-specified list of symbols. |
| mpl_delete_Morphy | Destroys an instance of a Morphy object. |
| mpl_delete_rawdata | Deletes the caller-input data. |
| mpl_first_down_recon | Reconstructs the first (downpass) nodal reconstructions |
| mpl_first_up_recon | Reconstructs the second (uppass) nodal reconstructions. |
| mpl_get_charac_weight | Retrieve the weight of a character in the dataset |
| mpl_get_gaphandl | Get / set gap handler from a Morphy object. |
| mpl_get_num_charac | Retrieve the number of character (columns) in the dataset. |
| mpl_get_num_internal_nodes | Gets the number of internal nodal reconstruction sets being... |
| mpl_get_numtaxa | Retrieve the number of taxa (rows) in the dataset. |
| mpl_get_symbols | Retrieves the current list of symbols. |
| mpl_init_Morphy | Sets up the dimensions of the dataset. |
| mpl_new_Morphy | Creates a new instance of a Morphy object |
| mpl_second_down_recon | Performs the second nodal reconstructions for characters with... |
| mpl_second_up_recon | Finalises the ancestral state reconstructions for characters... |
| mpl_set_charac_weight | Set the weight of a character in the dataset |
| mpl_set_num_internal_nodes | Sets the number of internal nodes in the dataset |
| mpl_set_parsim_t | Sets a character's parsimony function type |
| mpl_translate_error | Converts a numeric error code to human-readable format |
| mpl_update_lower_root | Updates the nodal sets for a lower ("dummy") root node |
| mpl_update_tip | Initial update of tip values following uppass reconstruction. |
| NNI | Nearest neighbour interchange (NNI) |
| PhyDat2Morphy | Initialize a Morphy object from a 'phyDat' object |
| PlotCharacter | Plot the distribution of a character on a tree |
| PrepareDataProfile | Prepare data for Profile Parsimony |
| profiles | Empirically counted profiles for small trees |
| QuartetResolution | Relationship between four taxa |
| RandomMorphyTree | Random postorder tree |
| RandomTreeScore | Parsimony score of random postorder tree |
| Ratchet | Parsimony Ratchet |
| RearrangeEdges | Rearrange edges of a phylogenetic tree |
| referenceTree | Tree topology for matrix simulation |
| SingleCharMorphy | Morphy object from single character |
| SiteConcordance | Calculate site concordance factor |
| SPR | Subtree pruning and rearrangement (SPR) |
| StepInformation | Information content of a character known to contain _e_ steps |
| StopUnlessBifurcating | Check that all nodes in a tree are bifurcating. |
| Suboptimality | Tree suboptimality |
| SuccessiveApproximations | Tree search using successive approximations |
| summary.morphyPtr | Details the attributes of a morphy object |
| TaxonInfluence | Rank taxa by their influence on phylogenetic results |
| TBR | Tree bisection and reconnection (TBR) |
| TBRWarning | TBR Warning Print a warning and return given tree |
| TreeLength | Calculate the parsimony score of a tree given a dataset |
| TreeSearch | Search for most parsimonious trees |
| UnloadMorphy | Destroy a Morphy object |
| WhenFirstHit | When was a tree topology first hit? |
| WithOneExtraStep | Number of trees with one extra step |
