As the past two posts have attested, we are on the cusp of doing some actual, real-life analysis. If at all possible, I want to run the analyses using freely available, open source software. Fortunately, all of the major software packages for phylogenetically-informed, quantitative analaysis are free! Here are the ones I’m looking at:
- For constructing trees and some simple analyses: Mesquite. (all of the tree plots you’ve seen have been done in this program)
- For general statistical analysis: R, along with the smatr, ape and ggplot2 packages. I will make a serious effort to post all scripts that are used to generate graphics and analyses; I would encourage all of you to do the same.
- For additional analysis of quantitative data in a phylogenetic context: COMPARE.