All functions

DengueBEASTMCC

Dengue fever BEAST MCC tree

DengueSeqs

Dengue fever sequences

DengueTrees

BEAST analysis of Dengue fever

.render.server.info()

Auxiliary functions

findGroves()

Identify clusters of similar trees

findMRCIs()

Find MRCIs

fluTrees

BEAST analysis of seasonal influenza (A/H3N2)

linearMrca()

Linear MRCA function

makeCollapsedTree()

Collapse a tree into a single tip per category

medTree()

Geometric median tree function

multiDist()

Metric function for multiPhylo input

plotGroves()

Scatterplot of groups of trees

plotGrovesD3()

Scatterplot of groups of trees using scatterD3

plotTreeDiff()

Plot tree differences

refTreeDist()

Metric function for comparing a reference phylo to multiPhylo input

relatedTreeDist()

Tree distance when trees have "related" tips

simulateIndTree()

Simulate randomised "individuals" tree

tipDiff()

Find tip position differences

tipsMRCAdepths()

Tip-tip MRCA depths

treeConcordance()

Tree concordance

treeDist()

Metric function

treeVec()

Tree vector function

treespace()

Phylogenetic tree exploration

treespaceServer()

Web-based tree explorer

wiwMedTree()

Median transmission tree

wiwTreeDist()

Transmission tree distance

woodmiceTrees

Bootstrap trees from woodmouse dataset