Man pages for ms609/TreeSearch
Phylogenetic Tree Search Using Custom Optimality Criteria

AddTipAdd a tip to a phylogenetic tree
AllAncestorsList all ancestral nodes
AncestorEdgeAncestral edge
BootstrapTreeBootstrap tree search with inapplicable data
BootstrapWeightingsBootstrap Weightings
C_FitchWrapper to FITCH
C_Fitch_ScoreFitch Score Calculate the parsimony score of a tree (number...
C_Fitch_StepsFitch steps
CladeSizesClade sizes
CladewiseReorder tree Cladewise
C_node_depthnode depth Wrapper for the ape function
DescendantEdgesDescendant Edges
DoSectorialSectorial Search with inapplicable data
EdgeAncestryEdgeAncestry
EnforceOutgroupForce taxa to form an outgroup
FitchFitch score
ListToMatrixEdge list to edge matrix
Lobo.dataRaw data from Zhang et al. 2016
Lobo.phyData from Zhang et al. 2016 in phyDat format
NeworderPhyloneworder_phylo Wrapper for the ape function
NeworderPruningwiseneworder_pruningwise Wrapper for the ape function
NJTreeNeighbour Joining Tree
NNINNI
OrderEdgesNumberNodesOrder edges and number nodes Wrapper for the C function
RandomTreeGenerate random tree topology from dataset
RatchetParsimony Ratchet
RearrangeTreeRearrange phylogenetic tree
RenumberRenumber a tree's nodes and tips
RenumberTipsReorder tips
RenumberTreeRenumber tree Order edges and number nodes Wrapper for the C...
SampleOneQuick sample
SectorHasDataSector Data Check that chosen sector contains...
SectorialSectorial Search
SingleTaxonTreeSingleTaxonTree
SPRSubtree Pruning and Rearrangement
SuboptimalityTree suboptimality
SubtreeExtract subtree
SuccessiveApproximationsTree Search using Successive Approximations
SuccessiveWeightsSuccessive Weights
TBRTBR
TBRWarningTBR Warning Print a warning and return given tree
TipsAreNamesExtract character data from dataset
TreeSearchSearch for most parsimonious trees
ms609/TreeSearch documentation built on Nov. 29, 2017, 8:24 a.m.