Berkeley INTEGBI 200A - THE BASICS OF NONA, WINCLADA AND TNT (4 pages)

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THE BASICS OF NONA, WINCLADA AND TNT



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THE BASICS OF NONA, WINCLADA AND TNT

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Lecture Notes


Pages:
4
School:
University of California, Berkeley
Course:
Integbi 200a - Principles of Phylogenetics: Systematics
Principles of Phylogenetics: Systematics Documents

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Integrative Biology 200A PRINCIPLES OF PHYLOGENETICS University of California Berkeley 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



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