DOWNLOADING AND UNLOCKING WINCLADA, NONA, AND TNTWINCLADA MATRIX MANIPULATIONSPARSIMONY RATCHET EXERCISEIntegrative Biology 200A University of California, Berkeley PRINCIPLES OF PHYLOGENETICS Spring 2008 Lab 4 THE BASICS OF NONA, WINCLADA AND TNT NONA (No Name; Goloboff 1999) [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 1999-2002) [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 2000) [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 tax a. 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. DOWNLOADING AND UNLOCKING WINCLADA, NONA, AND TNT - Make a new folder on the desktop - Go to www.cladistics.com/downloads - Download all three programs, and some sample data, to your new folder. Here’s how: - WinClada: Click on WinClada, scroll to the bottom, click Download WinClada, Click WINCLADA.EXE, save to your new folder. - Also on this page, download the sample data by clicking: Sample files, compressed self-extracting. Save them to your new folder. - Nona: Click on Nona, Click on Download Nona, click Pars-win.exe, save Pars-win.exe to your new folder. - TNT: Click TNT, click TNT Download, click TNT, click Win (menu interface), save ziptnt.exe to your new folder.- WinClada is ready to go, but the other two programs, and the sample data, still need to be extracted. Double-click on Pars-win.exe. A command line program will run briefly, then your folder will fill up with lots of new programs and other stuff. - Do the same for ziptnt.exe - Do the same for samples.exe - There is still one more step – registering Nona. Go to Start Menu > Programs > Accessories > Command Prompt. The command prompt will appear. Change directory to your new folder: cd Desktop\New Folder should work. Now, enter the exact string wconvert winona yatasto and your name (to register the program to you) or IB 200 A (to register the program with the class). - Now we’re ready to use the programs. WINCLADA MATRIX MANIPULATIONS Open WinClada by clicking the WinClada icon in your new folder in the Program menu. Once in WinClada, select the “File” menu and then “Open file”. Open the sample file sampldna.ss. 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, (WINONA.EXE) 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
View Full Document
Unlocking...