News: 2011 bioblitz!
Farrell Lab undergraduate Adam Clark is leading the second annual Harvard bioblitz. Join us on May 1! More
News
Prof. Farrell co-authors new paper which answers longstanding scientific question about cause of tropics' stunning biodiversity. MoreCurrent research
Current research extends the evolution of insect-plant interactions to other trophic levels through a broad collaboration in the beetle Tree of Life project.
A new research dimension in the lab concerns the acoustic signals produced for mating and territory defense. More
Phylogenetic analysis
Each item in this section includes PAUP batch files or commands where appropriate. This is not an exhaustive manual, nor are the techniques original. These are just some of approaches which our lab has found generally useful. Some useful references which provide broader overviews are Phylogenetic Trees Made Easy by Barry Hall and Molecular Systematics, 2nd Edition, edited by David Hillis, Craig Moritz, and Barbara Mable. PAUP also has a quick start tutorial on its web page.
*This section was last updated on December 2, 2009, though most of its information has not been updated since June 10, 2002.
This section includes:
- NEXUS file prep.
- Batch files
- Homogeneity testing
- Saturation plots
- Searches
- Decay indices
- Likelihood model choice
- Molecular clock testing
- Calibrating methods
- Errors on node times
- Hypothesis testing
Flowchart of strategies for phylogenetic analysis
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