# Statistical Exploration of Landscapes of Phylogenetic Trees

## Documentation for package ‘treescape’ version 1.10.18

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

DengueBEASTMCC | Dengue fever BEAST MCC tree
DengueSeqs | Dengue fever sequences
DengueTrees | BEAST analysis of Dengue fever
findGroves | Identify clusters of similar trees
findMRCIs | Find MRCIs
fluTrees | BEAST analysis of seasonal influenza (A/H3N2)
linearMrca | Linear MRCA function
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
tipDiff | Find tip position differences
treeDist | Metric function
treescape | Phylogenetic tree exploration
treescapeServer | Web-based tree explorer
treeVec | Tree vector function
wiwMedTree | Median transmission tree
wiwTreeDist | Transmission tree distance
woodmiceTrees | Bootstrap trees from woodmouse dataset