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Tree editing and ploting tools in Arbor (Tip labels utilities (Extract…
Tree editing and ploting tools in Arbor
Tree plots
Single tree
PlotTreeWithAPE_ExportTree_Bob (Cornell_BobT): {Plot and export String}
plotTreeWithggtree-app (fxArborApps): Plot Tree with ggtree
PlotTreeWithAPE (fxPhylogenyTools): plot tree using ape
plot from Nexus (fxPhyogenyTools): Plot and wrap the result in a PNG for output on the webpage
rescalePhylo (fxPhylogenyTools): rescale the plot of a tree using maximimum branching time
hclustDendrogram (fxPhylogenyTools):
With traits
Generate PhyloTrait Rendering (fxPhylogenyTools): Create a hierarchical Heatmap input file from a tree and matrix
Hierarchical Heatmap from Tree and Matrix (fxPhylogenyTools): Create a hierarchical Heatmap input file from a tree and matrix
PlotTraits (fxPhylogenyTools):
Compare trees
cophylo-app (fxArborApps): Plot of two phylogenetic trees side by side with lines connecting pairs of interacting species
Congruify (fxPhylogenyTools): Congruification
cophylo (fxPhylogenyTools):
compareTrees (fxPhylogenyTools): plot two different trees
Tree formating and editing
Tree editing
Convert Tree to Hierarchy Table (fxPhylogenyTools): Convert Tree to Hierarchy Table
Read Nexus Taxonomy Tree - Force Binary (fxPhylogenyTools):
Read Nexus Trees using rncl (fxPhylogenyTools): Read Nexus Trees using rncl
convert nexus string to ape phylo (fxPhylogenyTools)
Tree formating
Graft Tree Onto Named Node (fxPhylogenyTools): Graft a subtree onto a receiving tree, at a given node
Make Fake Branch Lengths (fxPhylogenyTools): Computes fake branch lengths with R compute.brlen() from ape
ResolvePolytomy (fxPhylogenyTools): resolve multichotomies randomly in phylogenetic trees with ape
collapseSingles (fxPhylogenyTools):
removeDuplicateTipsFromTree (fxPhylogenyTools):
Phylogentic distance
Mean Nearest Taxon Distance (phyloCommunityEcology):
MNTD-scratch (CornellCole): Calculate mean nearest taxon distance
Tip labels utilities
Extract labels info
Extract Genus from tree tip names (fxPhylogenyTools): Extract Genus from tree tip names
Tip Names from Nested Tree (fxPhylogenyTools): traverse a tree in nested format and output a single column table with species names from the tree taxa
getTipNames (fxPhylogenyTools):
Match Labels and tables
aRbor tree table match (fxPhyologenyTools):
matchTreeData (treeTraitMatching): A function to match the tree and data
Make Tree Tips Match Matrix (fxPhylogenyTool): Make Tree Tip Names Match Matrix
Renaming tips
Rename Tree Tips to Genus species(fxPhyloMap): Rename the tree tips to have the form Genus species
takeOutCharacterFromNames (fxPhylogenyTools):
renameTreeTips (fxPhylogenyTools):
Character descriptives and utilities
dconsistencyIndexAllChars (fxPhylogenyTools): Compute consistency index
parsimonyScoreAllChars (fxPhylogenyTools): Get parsymony scores for all charachters
predictMissingDiscrete (fxPhylogenyTools): Predict missing discrete characters
OpenTree, PhyloMap and TimeTree utilities
OpenTree utilities
Return the OpenTree subtree from a table of OTL node IDs (Cornell_BobT):
Create Matched Induced Tree and Matrix from Table (fxOpenTree): Create Matched Induced Tree and Matrix frim Table
Created Inferred Tree from species list (fxOpenTree): Extract a tree from OpenTreee with taxa from a species list description
Explore OpenTree species name completion (fxOpenTree): Consults the OpenTree API and extracts canonical names from the OpenTree taxonomy
Explore Study Trees (Return Tree Info) from Taxon Name (fxOpenTree): Consults the OpenTree API and extracts canonical names from the OpenTree taxonomy
TreeTimerBobConvert2 (zarborSBU): Takes a list of taxa and matches them to the OpenTree of life taxonomy
BobGetOpenTreeFromOTL_IDs (Cornell_BobT):
PhyloMap utilities
Merge Tree, Occurrences Table, and Morphology Table for PhyloMap (fxPhyloMap): Scans through a species occurence table and add location observations
WF Combine Morph Location Matrix and Tree nto PhyloMap (fxPhyloMap): The Workflow processes an occurrence matrix and a tree into phylomap
TimeTree utilities
Match taxa to the TimeTree of Life (timetreeMaker): Match a list of taxa to the OpenTree of life taxonomy