Collection of scripts, functions, methods for building and analysing tree diagrams in R.
- UPGMA
- NJ
- Ultrametric and binary tests
- Tree shape metrics
Tips and Notes:
If a tree is hard to read, transform the edge lengths by sqrt (this keeps relative lengths whilst making nodes easier to see) tree$edge.length <- sqrt(tree$edge.length)
Phangorn tutorial:
https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.html#molecular-dating-with-a-strict-clock-for-ultrametric-and-tipdated-phylogenies