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Integrative Biology 200B Spring 2009

"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"

Lab Prep 2: BEAST

TreeEdit is now available for Macs.  Download the zip file below.  The fact that this is only Mac software will make running this lab on PC even more difficult.  Although you may be able to do the TreeEdit stuff in Mesquite.

I will not be printing out todays handout cause it is so long.  You may want to download it.

Hi everybody, sorry for the delay.

This lab will be taught in Mac OS.  That does not mean that you can't use Windows, but it does mean that Brian will not be dealing with problems in Windows.  Therefor, if you have a PC, you may want to team up with a friend who has a Mac.

Future labs will be for both Mac and PC. 

TextWrangler is only for Macs, but I believe that it is just a text editor, so PC users can just use WordPad or NotePad.  However, as I already stated, Brian is not going to help with PC specific problems for this lab, so you may want to double up on Macs.

For Thursdays lab you will need the following software:

Required Software:
(1) the 'BEAST bundle' (BEAST v.1.4.8, BEAUti v.1.4.8, logCombiner v. 
1.4.8, TreeAnnotator v.1.4.8) http://beast.bio.ed.ac.uk/Programs

(2) Tracer v.1.4.1 http://tree.bio.ed.ac.uk/software/tracer/

(3) FigTree v.1.2.1 http://tree.bio.ed.ac.uk/software/figtree/

(4) Download this zip file of TreeEdit for Mac, unpack it and make sure that it runs.

(5) TextWrangler v.2.3 + http://www.barebones.com/products/TextWrangler/download.html


You also should down load and unpack the following zip file with the tutorial data sets tutorial_files.