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Berkeley INTEGBI 200A - THE BASICS OF NONA, WINCLADA AND TNT

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EXERCISESWINCLADA MATRIX MANIPULATIONSPARSIMONY RATCHET EXERCISEIntegrative Biology 200A University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS" Spring 2006 THE BASICS OF NONA, WINCLADA AND TNT NONA (No Name; Goloboff 1993a) [http://www.cladistics.com] is a very efficient PC program for parsimony analysis, i.e. searching for shortest trees, (a Macintosh version is also available). NONA has a command prompt interface. This program has no maximum limit for the number of taxa and/or characters. The trees are internally treated as fully dichotomous, but the default option shows only the branches that are unambiguously supported. It also allows one to define the initial tree (“seed”) or to choose a random tree for different strategies in exploring tree space. WINCLADA (Nixon 2003) [http://www.cladistics.com] is a Windows-based program that allows one to enter and edit data to be analyzed with NONA. This includes, for example, adding and editing names of characters, character states and/or taxa, modifying the character coding, deactivating/activating characters, and aligning molecular data by eye. Although these functions can be accomplished using a text editor program, WinClada was specifically designed for constructing data matrices for cladistic analyses and is much more convenient for these purposes. In addition, WinClada allows one to visualize and edit trees obtained with NONA. This includes, for example, mapping character states onto a tree, moving and/or collapsing branches, choosing alternative rootings and/or optimizations, calculating bootstrap values and consensus trees, editing the trees for printing or outputting them to a vector graphics program. Finally, WinClada can be used to construct and use multi-entry identification keys. TNT (Goloboff, Farris and Nixon ????) [http://www.cladistics.com] is a program available for Windows, MacOS or Linux. It has very efficient tree-searching algorithms for large data sets of 300 to 500 taxa. Parsimony is the only available optimality criterion. It implements many new heuristic search methods, such as the ratchet and sectorial searches. It can also be used for tree manipulation and diagnosis. As it is optimized for large matrices it is probably not the best program to use for data sets with fewer taxa. EXERCISES WINCLADA MATRIX MANIPULATIONS First you need to take the WinClada example file off the server and put it on the desktop. The file can be found in IB Computer Lab Shared Folder > IB200A > WinClada. Copy the file Matrix Named and paste it onto the desktop. Open WinClada by clicking the WinClada icon in the IB200a folder in the Program menu. Once in WinClada, select the “File” menu and then “Open file”. By default, WinClada wants to open a .ss or .winc file, so select show all files and select your .txt file. Open the Matrix Named.txt file. WinClada works like other Windows-based programs. You can use the mouse to select the options under each menu or a combination of key strokes.Now you can execute as many functions as you wish. Note that this program has a feature to protect the matrix against “typos”, so if you want to actually modify data you have to select “Unlocked” under the “Edit” menu. WinClada can read and write matrix files in a variety of formats including: *.ss (Hennig86/NONA); *.winc (WinClada—an expanded *.ss format that includes WinClada preferences and specific commands); *.nex (PAUP/MacClade format); and *gde/*.fst (generic DNA sequence formats). NONA can read only *.ss formatted files directly. You should explore the functions under each main menu at the top of the screen. RUNNING NONA FROM WINCLADA There are two ways to launch NONA from WinClada: 1) Select the “Analyze” menu; select “Spawn” then “NONA”. Select “enter path” (you need to tell WinClada where NONA resides on your computer). Navigate to the NONA icon, select it, and click “Open”, then put the current path as a default. Next, return to Analyze – Spawn – NONA – then “Submit Current Matrix”. WinClada will display a “Current Character Settings” window (0 characters should be deactivated, 28 characters should be additive, and the average character weight should be 0.857). Click “yes” and NONA will launch. To exit NONA, type “quit” or “z.” 2) Select the “Analyze” menu, then select an option (e.g. “Heuristics”) and enter the appropriate values. NONA will be spawned and proceed with an analysis as instructed by WinClada. When the analysis is complete, NONA will close and return the results to WinClada automatically, displaying the output trees in the tree-viewing (“winClados”) window. To change from the tree window to the matrix window choose the “Interface” menu and select “winDada”. Once you understand how to enter and exit NONA, submit your data to NONA. Select the “Analyze” menu, then “Spawn”, “NONA”, and “Submit Current Matrix.”. Once in NONA, type the following commands (each command should be followed by a semicolon “;” and the <enter> key. Type: help; This will display a list of all the commands and arguments. whennig; (or “w;”) at the command line. This will calculate a Wagner tree. You will be presented with information about the tree (its length) but you will not see the tree until you type: tplot; (or “tp;”)The tree should then be printed to the screen. This tree, obtained with the command “whennig;”, is not necessarily the shortest tree. In order to save the tree to a file, use the command: sv* my.tre sv/; (where “my.tre” is the name of the file, e.g. “brent.tre”). Now exit NONA (type “z;”) and return to WinClada. WINCLADA TREE MANIPULATIONS In WinClada, open the tree you saved by going to the “File” menu and selecting “Open Tree file.” Find the file and open it. The tree will appear in the tree window (winClados) of WinClada. 1. The spacing and appearance of the branches can be changed with the function keys: F2 and <shift> F2 change the thickness of the branches F3 and <shift> F3 change the horizontal spacing F4 and <shift> F4 change the vertical spacing2. The arrow keys can be used to move the tree around the screen (note: the tree is treated as a graphics object—not a text object—so the up arrow moves the tree up the screen, not down—as you would expect if you were scrolling in a text editor). 3. Practice changing the


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Berkeley INTEGBI 200A - THE BASICS OF NONA, WINCLADA AND TNT

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