MacClade_Mesquite - Integrative Biology 200A...

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University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS" Spring 2008 Lab 1: Introduction to Character Matrices Introduction Today we will learn the basics of putting together a character matrix. The main tools we’ll be using will be MacClade and its descendant, Mesquite. These two programs make it easy to put together a data matrix with all the great characters you’ll soon be coming up with. Both programs were developed by Wayne and David Madison, twin brothers who are both professors of phylogenetics. MacClade, the original program, is, as the name suggests, only for Macs. After many years of selling MacClade commercially, and updating it in their spare time, the Madisons decided to branch out and create Mesquite, a free, open-source, Java-based program that works on any platform. Neither program is used to actually infer phylogenies (although MacClade does have some very basic, outdated ways of doing this.) Instead, they are used for creating and editing data matrices, examining the distribution of characters on a phylogeny, and testing hypotheses about character evolution. Either program makes a great starting point, because they allow you to collect and organize characters and taxa (I mean, semaphoronts.) Another reason we’re starting with these data-matrix programs is that they’re a great way to explore the data you’re about collect for your term paper project. Both MacClade and Mesquite can be found on the computers we’ll be using today, by following the path: Macintosh Hard Drive > Applications > 200A . MacClade To open MacClade, go to Macintosh Hard Drive > Applications > 200A > MacClade . When you double-click on the multi-colored phylogeny icon, MacClade will load and after a few moments, a window will ask you what file you’d like to open. Today, we’ll be using an example file that came with Mesquite, just so you all can see what a filled-in, working data matrix looks like. Follow this path to open the file: Macintosh Hard Drive > Applications > 200A > Mesquite_Folder > examples > Ancestral_states > 01-DataMatrix.nex . MacClade is designed around two main windows, the tree window and the data editor window. Two other windows we will see today are the chart window and the character status window, although they are of less importance. The first window you’ll see today is the tree window, which shows that this file already has a phylogenetic reconstruction stored with it. Of course, a newly-made data matrix won’t have any phylogeny stored with it yet, but we’ll get to that later. The tree is shown with scaled branch lengths and character reconsrutcions plotted on it. This can be changed using the display menu, which includes such options as “change tree type” and “change font.” Feel free to explore some of these options and see how the way the tree looks changes. 1
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This note was uploaded on 08/01/2008 for the course IB 200 taught by Professor Lindberg,mishler,will during the Spring '08 term at University of California, Berkeley.

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MacClade_Mesquite - Integrative Biology 200A...

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