I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc. Please comment if you have code for doing bayesian phylogenetic inference in R. I know phyloch has function mrbayes, but can’t get it to work… Phylogenetics in R View more presentations from schamber
The phangorn package is a relatively new package in R for the analysis and comparison of phylogenies. See here for the Bioinformatics paper and here for the package. Here is an example of using phangorn from getting sequences to making phylogenies and visualizing them: Getting sequences from Genbank Multiple alignment Maximum likelihood tree reconstruction Visualizing trees Visualizing trees and traits Make fake traits: Visualize them on trees: ...