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Tree editing and ploting tools in Arbor (Tree plots (PlotTreeWithAPE…
Tree editing and ploting tools in Arbor
Tree plots
PlotTreeWithAPE_ExportTree_Bob (Cornell_BobT): Plot and Export String
cophylo-app (fxArborApps): Plot of two phylogenetic trees side by side with lines connecting pairs of interacting species
plotTreeWithggtree-app (fxArborApps): Plot Tree with ggtree
Congruify (fxPhylogenyTools): Congruification
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. An output table is created containing the pathname to
PlotTraits (fxPhylogenyTools):
PlotTreeWithAPE (fxPhylogenyTools): plot tree using ape
cophylo (fxPhylogenyTools):
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
compareTrees (fxPhylogenyTools): plot two different trees
hclustDendrogram (fxPhylogenyTools):
Tree editing
Convert Tree to Hierarchy Table (fxPhylogenyTools): Convert Tree to Hierarchy Table
Read Nexus Taxonomy Tree - Force Binary (fxPhylogenyTools):
Read nNexus Trees using rncl (fxPhylogenyTools): Read nNexus Trees using rncl
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
multi2di (fxPhylogenyTools): resolve multichotomies randomly in phylogenetic trees with ape
collapseSingles (fxPhylogenyTools):
removeDuplicateTipsFromTree (fxPhylogenyTools):
convert nexus string to ape phylo (fxPhylogenyTools)
Phylogentic distance
Mean Nearest Taxon Distance (phyloCommunityEcology):
MNTD-scratch (CornellCole): Calculate mean nearest taxon distance
Tip labels utilities
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
aRbor tree table match (fxPhyologenyTools):
matchTreeData (treeTraitMatching): A function to match the tree and data. Returns a phylogeny and data frame with matched tips and row orders. Taxa not in both the tree and the table are dropped.
Make Tree Tips Match Matrix (fxPhylogenyTool): Make Tree Tip Names Match Matrix
getTipNames (fxPhylogenyTools):
Rename Tree Tips to Genus species(fxPhyloMap): This analysis is an algorithm to read in a tree and rename the tips to have the form Genus species" without any further curator, year, and with spaces between the names, not an underscore.
takeOutCharacterFromNames (fxPhylogenyTools):
renameTreeTips (fxPhylogenyTools):
Match taxa to the TimeTree of Life (timetreeMaker): This function takes a list of taxa and matches them to the OpenTree of life taxonomy. It then matches these taxa to the TimeTree of Life using taxonomy, and swaps out as many exchangeable taxa as possible using the Phyndr algorithm to obtain a time-calibrated phylogeny with maximal overlap with the original taxa list.
Character descriptives and utilities
dconsistencyIndexAllChars (fxPhylogenyTools): Compute consistency index
parsimonyScoreAllChars (fxPhylogenyTools): Get parsymony scores for all charachters
predictMissingDiscrete (fxPhylogenyTools): Predict missing discrete characters
OpenTree and PhyloMap utilities
OpenTree utilities
BobGetOpenTreeFromOTL_IDs (Cornell_BobT):
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: this analysis expects a comma separated list consisting of scientific names.
Explore OpenTree species name completion (fxOpenTree): The analysis consults the OpenTree API and extracts canonical names from the OpenTree taxonomy.The output table consists of several columns containint the OpenTree name and taxonomy ID and other relevant information.
Explore Study Trees (Return Tree Info) from Taxon Name (fxOpenTree): This analysis expects a comma separated list consisting of scientific names.The analysis consults the OpenTree API and extracts canonical names from the OpenTree taxonomy. The output table consists of several columns containint the OpenTree name and taxonomy ID and other relevant information.
TreeTimerBobConvert2 (zarborSBU): This function takes a list of taxa and matches them to the OpenTree of life taxonomy. It then matches these taxa to the TimeTree of Life using taxonomy, and swaps out as many exchangeable taxa as possible using the Phyndr algorithm to obtain a time-calibrated phylogeny with maximal overlap with the original taxa list.
PhyloMap utilities
Merge Tree, Occurrences Table, and Morphology Table for PhyloMap (fxPhyloMap): This analysis step scans through a species occurence table (of the format of Chodon's Heliconia location table) and tries to add as many of these location observations as possible to the taxa of an input phylogenetic tree. Species name and collection number are used to try to find matches. The output tree has the locations added as attributes so they can be traversed using phyloTraitMap and support interactive exploration.
WF Combine Morph Location Matrix and Tree nto PhyloMap (fxPhyloMap): The Workflow processes an occurrence matrix and a tree into phylomap. Both sources are forced to have "Genus species" format names so matching can be performed.