Software
Lagrange: likelihood analysis of geographic range evolution
Lagrange is a Python package, co-authored by Stephen Smith, implementing dispersal-extinction-cladogenesis models of geographic range evolution described in Ree et al., 2005 and Ree and Smith, 2008. It can be used to infer geographic ancestry (historical ranges) and estimate rates of dispersal and local extinction on phylogenetic trees that have species range data arrayed at their tips.
Phylografter: collaborative phylogenetic tree assembly
A web2py-based application that lets you combine source trees from published literature into large "megatrees." I developed this as part of a collaborative effort to understand ecological communities and functional traits of plants at a large phylogenetic scale, and used it successfully to graft together a tree of over 14,500 species of land plants, with every node in the grafted tree mapping directly back to a node in a published tree.
Stochastic mapping and key innovation tests (old)
Python code for stochastic mapping and key innovation tests. Not pretty, easy to use, or well documented. Please email me for advice in running this. Those wishing to test key innovation hypotheses should consider BiSSE (Maddison et al., 2007, Syst. Bio.)
- keyinnotest-20080208.tar.gz
- Standalone stochastic mapping code: stmap.tar.gz
Older stuff (gapcode.py, web utilities)
Simple utilites for phylogenetics:
- 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)
- Convert newick trees and data to Pagel format (Discrete, Multistate, etc.)
- Create PDF or EPS figures of trees
Tred - experiments in web-based tree editing
Tred is an ongoing experiment in using web2py as a web-frontend to existing code - in this case, to view and make PDF figures of trees, including multi-page PDFs.
