13_Trees_Lab - Integrative Biology 200A Principals of Phylogenetics University of California Berkeley Spring 2006 The What the Hell Do I Do with

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Integrative Biology 200A University of California, Berkeley Principals of Phylogenetics Spring 2006 The What the Hell Do I Do with All These Trees Lab We’ve generated a lot of trees in the last few weeks. Today we’re going to explore different ways to view, compare, and manipulate those trees. First we’re going to use TreeView to look at a consensus tree generated in MrBayes . Then we’re going to compare a bunch of trees with the same taxa but different topology using PAUP* and generate several types of consensus trees. Finally we’re going to generate a consensus tree from trees that have overlapping but not identical taxa using Matrix Representation with Parsimony. We’re going to be using many different files for this lab. Find them online at the 200A Syllabus and Handouts page. TreeViewX By now you will have noticed that most of the programs that generate trees either don’t print trees at all or make really crappy ones. Luckily there are a lot of different ways to view trees. Today we’ll be using TreeViewX (which you have already used a few times.) It seems to be a little quirky. There are some files I have exported with branch lengths from PAUP that nonetheless do not appear to have branch lengths in TreeViewX. You may also want to try plain TreeView if you are a PC or MacClassic user. If something isn’t working, it is always worth opening it in Mesquite, exporting it in a few different ways, and seeing if any of them work. Mesquite can also export trees as a PDF, they sometimes come out a bit odd but try adjusting all the parameters. But back to today’s lab and TreeViewX: 1. Download MrBayesCephalopodConsensus.nex from the web page. This is a consensus tree generated by MrBayes for the Cephalopod COI dataset we’ve been using. It has two trees in it with identical topology. The first has branch lengths and node support values. The second has only branch lengths. 2. Open TreeViewX and open MrBayesCephalopodConsensus.nex in it. 3. Pull down the style menu and change the font size, so that you can easily read the names. 4. Push (the radial tree button) at the top of the page. You will see your tree as an unrooted tree. 5. Push the phylogram button and the internal labels button. The tree should now appear as a square phylogram with branch lengths that can be seen in the lengths of the branches and node support values as numbers.
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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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13_Trees_Lab - Integrative Biology 200A Principals of Phylogenetics University of California Berkeley Spring 2006 The What the Hell Do I Do with

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