Lab7_IntrotoPAUP - Integrative Biology 200A...

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1 Integrative Biology 200A University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS" Spring 2008 Lab 7: Introduction to PAUP* Today we will be learning about some of the basic features of PAUP* ( P hylogenetic A nalysis U sing arsimony [ * and other methods]), a phylogenetics program developed by David Swofford. Supposedly, it is pronounced “pop star.” PAUP* can infer phylogenies using distance, parsimony and likelihood. Today, we will run these types of analyses using a sample mtDNA data set. We will learn how to use more features in PAUP* in later labs. EXERCISE I: Basic PAUP. Before we get started, a word about preparing files for use in PAUP. PAUP takes a nexus (.nex) file as input. You can edit these files with a text editor (such as Notepad or Text Wrangler) or with MacClade or Mesquite. It is easy to make nexus files if you know what to put. Ask me if you want to know more about the nexus file format. Open PAUP*. Open PAUP*. You'll find it in Macintosh HD>Applications>200A >paup> paup4b10-x86-macosx . Command-line PAUP runs through the terminal window. First, we are going to analyze a sample file that will allow us to build a primate phylogeny, primate-mtDNA.nex. Type execute then drag-and-drop the primate-mtDNA.nex file into the terminal window. This will input the file path without you having to type the whole thing. Press return. PAUP will tell you a few things about the file: how many taxa and characters it has in it, and what nucletotide ambiguity codons are being used. For instance, right now "R" is treated as either an A or G for analytical purposes. Let's find out a little bit about our file. First, we'll get a brief summary of the character status. First, we’re going to look at the character summary. Type cstatus then press enter. (Menu equivalent: DATA menu, Show character status (Brief summary.) ) The output tells you the current optimality criteria (parsimony, likelihood or distance), the number of characters, the character status, coding, number of parsimony informative characters, etc. These are some of the basic summary statistics of your data. Now, we'll look at the pairwise distance between the taxa. Type showdist This is useful because it tells you how many differences there are between any two taxa. Taxa that have 0 distance between them can't be differentiated by PAUP. Since they have many equally parsimonious arrangements, they can make your analysis run for a very long time without getting closer to an optimal tree. So it is good to know in advance how many you are dealing with.
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Lab7_IntrotoPAUP - Integrative Biology 200A...

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