The instructions to process the results from Goloboff et al. (2009, Cladistics, 25:211-230) in a Windows machine (about 1GB RAM needed) follow below.
This used to require scripts, but after 2012, the commands to check taxonomy were incorporated into TNT as native commands. These instructions have been correspondingly updated (the old TNT web site, at http://www.zmuc.dk/public/phylogeny/TNT still contains the old instructions).
1) download the no-taxon limit version of TNT
2) download and install (e.g. from Control Panel, Fonts, Install New Font) the Tred font.
3) download and extract the data set and trees.
4) extract the contents from all previous four steps to the same directory (e.g. C:\TNT), run TNT, and accept the terms of the license.
ONCE IN TNT:
5) Typing taxonomy=;<enter> at the command line.
6) Open file Taxon_Names_Only.tnt
7) Open tree file (three files, *.tre extension) and select the tree you want to look at. For example, to process the best tree for the combined data set:
type at the command line: "tchoose 17"
8) Make sure that the text buffer is large enough to hold the entire tree figure; for this, type txtsize 20000 <enter> at the command line (you only have to do this once, TNT remembers between sessions).
PROCEDURE TO CHECK GROUPS ONE BY ONE IN TEXT-MODE:
first make sure pre-viewing of trees is off (with Format/PreViewTrees, it should not be ticked), and that the full taxonomy for each specioes is not displayed (typing taxname[! at the command line). Then you type at the command line:
taxonomy *0 Mammalia; view Mammalia;
make sure you don't leave a blank between the name of the taxon and the semicolon.
The cursor will be positioned at the closest group in the tree (if it exists, otherwise you get a message). The numbers displayed on the branch are the number of taxa in the reference group present in the tree, followed by the number of extraneous taxa (+) included in the closest group, and the number of members excluded (-). See Goloboff et al. 2009 for more details.
PROCEDURE TO COLOR SPECIFIC GROUPS IN THE TREE:
make sure pre-viewing of trees is ON, and then you type, e.g.:
taxonomy : 0 /Mammalia /Aves /Squamata ;
Once the tree is displayed, press "N" to not show taxon names and then "F" to fit tree to screen. Move tree with the arrow keys (and home/end). Press F5-F6 and F3-F4 to shrink/expand tree. If you press "G" and then click on a node, the group corresponding to that node will be displayed on screen. Press "M" to save tree-diagram to a metafile. Press "C" to toggle display of color codes for the different groups. Press "H" (help) for further options.