Integrative Biology 200A
University of California, Berkeley
PRINCIPLES OF PHYLOGENETICS
THE BASICS OF NONA, WINCLADA AND TNT
(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
(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
(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
Parsimony is the only available optimality criterion.
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.