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Integrative Biology 200B Spring 2009

"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"

Lab Prep 15: Biogeography

Lap prep for Thursday, April 16th

1. You need Mesquite. See old prep.

2. Download this file hafner88_Mesquite.nex

3. Download Treemap from: http://taxonomy.zoology.gla.ac.uk/rod/treemap.html

4. You may also need to download the files HAFNER88.NEX and HAFNER94.NEX if they did not come with your Treemap download

5. Download Lagrange and some other software to go with
it.  Follow Nick's instructions below:

Lagrange runs in Python.  Python is a free language/scripting environment
widely used in bioinformatics (BioPython), website management, etc. 
Programs written in Python are then platform-independent, because Python
can be installed on any operating system.

I. Mac OS X systems come with Python pre-installed (just type “python” at
the prompt in Terminal.app).  However, Lagrange needs some math/science
libraries (scipy, numpy) in addition to the basic Python, plus it is best
to use the most up-to-date version (Lagrange needs Python 2.4, many Macs
have Python 2.3 or older, type “python –V” to check).

So, the simplest thing to do is download everything you could ever need in
the free Enthought Python Distribution.  This is a single executable file,
you can get it here free as an educational user:

http://www.enthought.com/products/getepd.php

It is a ~300 MB download, so don’t everyone try and download it at once
during class on Airbears!  (it will download over wireless elsewhere, it
just takes awhile)

Once it is downloaded, double click and follow instructions to install.*

II. Download Lagrange from here and unzip it:

http://code.google.com/p/lagrange/

Place the “Lagrange” directory wherever you will be saving/editing your
data files (but keep those files outside of the Lagrange directory).