Richard Ree

Software

I’m a big fan of Python over other languages like C and Java. Python has many virtues that make it easy to quickly write useful code, from throwaway scripts to large web or gui applications. R is also very useful, but it is like having a screwdriver, whereas Python is the whole toolbox.

• Phylografter: Collaborative phylogenetic tree assembly. This is a web application that lets you combine source trees (e.g. from published literature) into large “megatrees.” View the demo or install it on your own computer.
• lagrange: Likelihood analysis of geographic range evolution. Developed in collaboration with Stephen Smith. An implementation of biogeographic inference methods described in Ree et al. (2005) and Ree and Smith, 2008.
  • More information, source code, downloads, etc.
• Stochastic mapping and key innovation tests (please email me for advice in running this).
• keyinnotest-20080208.tar.gz
• Standalone stochastic mapping code: stmap.tar.gz
• gapcode.py, a python script for coding indels in sequence alignments as binary characters for phylogeny reconstruction (version 2.1, 13 Jan 2008; thanks to Pieter Pelser for helpful suggestions)
• Web utilites for phylogenetics:
  • Convert newick trees and data to Pagel format (Discrete, Multistate, etc.)
  • Recode alignment gaps as binary characters (outdated; use gapcode.py instead)
  • Create PDF or EPS figures of trees