2009 Workshop

Please go to the following URLs and download the software. If you already have these applications please make sure that you have the latest version installed!

Before you do anything in phylogenetics, you're going to need a simple text editor. Text editors are key for manipulating the input and output files for most major software applications. Never use Microsoft Word as your text editor. We recommend the following text editors:

For Macs TextWrangler: http://www.barebones.com/products/TextWrangler/download.html
For PCs TextPad: http://www.textpad.com/

FigTree: http://tree.bio.ed.ac.uk/software/figtree/

Garli v. 0.951: http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html

MrBayes: http://mrbayes.csit.fsu.edu/

BEST: http://www.stat.osu.edu/~dkp/BEST/

Mesquite v.2.6: http://mesquiteproject.org/mesquite/download/download.html
The PDAP module for Mesquite: http://mesquiteproject.org/pdap_mesquite/index.html (Scroll down to "How To Download", read the instructions, and be sure to get PDAP for Mesquite 2 for your operating system.)

Brownie: Brownie.zip This is the command line version that will only run on a Mac.(no GUI). If you have a PC you are not likely to be able to run the current versions, the new version on the website (http://www.brianomeara.info/brownie) is currently non-functional but should be ready soon. See (http://www.brianomeara.info/brownie/manual) for the manual.

R: To download and install R and associated phylogenetics packages follow the instructions at Phylogenetics and Comparative Method in R. You must complete installation and the associated exercises on importing trees and comparative data if you'd like to follow along with Glor's hands-on demonstration of phylogenetic comparative methods on Tuesday morning.

The BEAST bundle: http://beast.bio.ed.ac.uk/Programs

BEAST v.1.4.8


BEAUti v.1.4.8


logCombiner v.1.4.8


TreeAnnotator v.1.4.8


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Phylocom: http://www.phylodiversity.net/phylocom/

This is a very brief guide to common things you might want to do. Note that logging in is required (though anyone can create an account).

• Editing Existing Pages - Go to the page you want to edit and click on the 'edit' link at the top of the page. (for really simple edits, you can just double click the block of text you want to change)
  

• Common editing tasks:
  

• editing text - Just type and delete text in the editor window then hit the 'save changes' button. There are some simple formatting directions below the editor (e.g. Bold, italics, etc.)
  

• creating links - to link to another page IN the wiki just type ["page name"] in an editor window, to link OUT of the wiki type [http://www.webpage.com] (note that quotes aren't used for linking out).
  

• uploading files - Click the 'upload files' button at the bottom of the editor window. Choose a file and give it a name in the 'Save as' box then hit the 'upload' button. Link to the file on your page by typing [[File(filename)]] in the editor window.
  

• displaying images - to display an image, upload it exactly the same way as with a file, then link to it by typing [[Image(filename)]] .
  

• Adding New Pages - Create a link from an existing page to the (currently non-existent) page you want to make by typing ["New Page's Title"], click on the link and hit 'Create this page'. Your new page will open in an editor window.
  

• Deleting Pages - First, think about whether or not the page really should be deleted. If so, hit the delete button at the bottom of the editing window.
  

If you want to play around to get a feel for how things work head over to the Wiki Sandbox.
More detail on editing can be found here