Lab4_NONA_Winclada - Integrative Biology 200A PRINCIPLES OF...

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Integrative 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. -
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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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Lab4_NONA_Winclada - Integrative Biology 200A PRINCIPLES OF...

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