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.

 

PREPARATION:

 

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) download the scripts to handle the trees.

5) 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:

 

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:

 

      select File/OpenInputFile

      select trees_molecules-morphology.tre

      type at the command line: "tchoose 17"

 

8) set display buffer (lower right corner of Settings/Memory) to 15000

9) make sure you have the "search" tool as visible, by clicking on Settings/Tools/ChooseTools, and then selecting the one with the magnifier (the last one).

 

Note: Steps 8 and 9 have to be done only 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 then you type at the command line:

 

     "dohi _Taxon_ "

 

For genera, skip the first underscore. 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. The last number is the number of SPR moves needed to make the reference group monophyletic.

    If you search for the string "YYYY" you will find the extraneous taxa included in the group, and if you search for "ZZZZ", the members excluded.  The string "XXXX" marks the closest group.

    If you type:

 

    "dohi _Taxon_ fullnames "

 

TNT will show the complete string of names (this helps to know what gets inside, or where the excluded members go!).

 

PROCEDURE TO COLOR SPECIFIC GROUPS IN THE TREE:

 

make sure pre-viewing of trees is ON, and then you type, e.g.:

 

   "colorgroups  _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.