Running TNT for Phylogenetic Analysis (on a Mac)

This blog post is meant to be informational. You can stop reading now if you don’t know what a cladistic analysis is and don’t care to ever know how to do one.

If you’re still reading, this post is written to provide what I’ve learned about getting TNT, a free phylogenetic analysis program, to work properly on a Mac. Bear in mind that I do not currently own a Mac. What I’m sharing with you is what we figured out as a class when I had my students use this program as part of a cladistics exercise.

TNT stands for Tree analysis using New Technology. This software is freely available from the Willi Hennig Society by following this link. There are lots of choices of downloads. If you’re using Windows, the Win (menu interface) is the easiest to use. The Win (charmode) is a command line only version of the software. I’ve not tried the Win (no taxon limit) version. For Macintosh, my students didn’t notice any difference between the Mac 32 and the Mac 64 (no taxon limit) versions. Both are command line only.

For any of these, you’ll click a link and download a ZIP file. You’ll need to extract the ZIP file before you start. In all versions, the data are stored in a .tnt file, which is a text file of the following format:

xread
‘Snowflakes 2013’
5 13
A 0 1 1 2 0
B 0 1 2 4 1
C 0 1 1 3 0
D 1 0 1 2 0
E 1 1 1 1 0
F 0 0 1 4 0
G 1 0 1 1 0
H 0 1 1 2 0
I 0 1 2 4 1
J 1 1 2 5 1
K 0 1 0 0 0
L 0 1 1 5 0
M 0 1 2 4 0
;

The text between the apostrophes is ignored by the program. The next line (5 13) indicates the number of characters (5) and the number of taxa (13) in the matrix.

We did notice that the first taxon listed (in this case ‘A’) will become the outgroup in your analysis. So, if you’ve already identified your preferred outgroup, it should be listed first.

The following lines list the taxon name first, followed by the character states for the five characters. The spaces aren’t necessary. There is a way to insert longer taxonomic names, but I didn’t bother with that. You can look at some of the example files that come with the software to determine how to do it. This is the bare bones data file.

You can prepare this file in any text editor. You can also do this within the menu interface version of TNT, but I think it’s easier to just type it in a text editor. This will save the file as a .txt file. For the command line versions of the software, you need to change the file extension to .tnt. The menu interface version doesn’t care what the file extension is.

If you’re working on Windows, your .tnt file needs to be in the same folder as the TNT software. If you’re on a Mac, your .tnt file must be in your username folder.

TNT has many capabilities, most of which are well beyond the scope of my little Principles of Paleontology class. There is a PowerPoint tutorial that comes with the menu interface version, if you want to learn more about it. In addition to this, especially for the command line only version, there is a TNT wiki available here.

Below, I’m going to cut and paste some instructions for a very simple analysis using both the menu interface and the command line versions of TNT. It turns out that the command line versions work essentially the same for both Windows and Mac.

Windows Menu Interface:

3) Open your data matrix
File–> Open input file
it’s probably not going to be a .tnt file. Check using all file types.

4) Run an analysis
Analyze–> Traditional Search
Use the defaults and click Search.
The dialog that appears tells you how many trees (=trees retained) of the shortest length (=’best score’) were found.

Wanna see your trees? Go to Format and uncheck preview trees. then got to Trees –> Display/save and accept the default. All your trees should appear.

5) Consensus
Next, let’s see where all the trees agree. Click the fourth icon from the left, where multiple trees are going into one.
Check the boxes beside Strict (=Nelsen) and Majority Rule (leave the cut-off at 50). Make sure Combinable Components and Frequency Diffs are unchecked.
Click OK

Two new trees will appear. The upper one is the strict consensus tree, where only branches in all of your most parsimonious trees are shown. The lower tree is the majority rule tree, where branches appearing 50 percent of the time will appear.

6) Mapping characters
If you want to know where the synapomorphies are on all these trees, TNT can show you.
Optimize–>Synapomorphies–>Map synapomorphies and accept the defaults. The synapomorphies will be mapped on the most parsimonious trees, numbered 0 through whatever, based on the order that you entered them in your matrix. Sometimes these things appear more than once, representing reversals.

7) Saving your results
This is where TNT fails a bit. One thing you can do is print the ‘display buffer,’ or all that text that appears when you execute a function. Go to File–>Output–>Print Display Buffer

Windows and Mac Command Line:

3) Open your data matrix
Type proc filename.tnt and hit enter.
1) The extension has to be .tnt (which I don’t know how to change on the Mac, but I can do on the PC)
2) The file needs to be in the username folder of your computer

4) Run an analysis
Type ienum ; and hit enter.
Yes, the semicolon matters and there needs to be a space between it and the command.
The dialog that appears tells you how many trees (=trees retained) of the shortest length (=’best score’) were found.

Wanna see your trees?
Type tplot ; and hit enter.
All your trees should appear.

5) Consensus
Next, let’s see where all the trees agree.
Type qnelsen ; and hit enter.
Type tplot ; and hit enter.

A new tree will appear. This is the strict consensus tree, where only branches in all of your most parsimonious trees are shown.

Type majority ; and hit enter.
Type tplot ; and hit enter.
This tree is the majority rule tree, where branches appearing 50 percent of the time will appear.

6) Mapping characters
Type map ; and hit enter.
A zillion trees will scroll by. The synapomorphies will be mapped on the most parsimonious trees, numbered 0 through whatever, based on the order that you entered them in your matrix. Sometimes these things appear more than once, representing reversals.

7) Saving your results
This is where TNT fails a bit.
In Windows, you can right click on the window and hit ‘select all.’ Then press enter. Then go to an open Word or text document and hit paste. Everything will be there. I don’t know if something similar can be done on a Mac.

 

Obviously, this is just a cursory treatment of TNT for phylogenetic analysis, but it should get you started. We did notice that this process worked fine on some Macs and on others, TNT would crash miserably. It seems there are operating system issues.

Anyone with further information to add to this, especially with regard to using it on a Mac, please let me know. I’m happy to revise this. I looked far and wide for something this simple to help me get started with TNT and there was nothing. So this is it. I hope other people find it helpful!

6 Comments

  1. Mark Schultz says:

    thank you. This is more helpful than their wiki!

    Like

    1. Penny says:

      I’m glad this is helpful to you!

      Like

  2. Jason Jung says:

    Thanks for this Penny! I know this has been up for a while, but I’ve been struggling learning TNT (well trying anyway) for my thesis work, but progress is slow.

    I wanted to let you know, if you haven’t come across this info in the intervening time, the way to get saved results on a mac is as follows:

    After entering the procedure (proc) command, enter another:
    log NAMEOFLOGFILE.txt ;

    You can use whichever name of course, and actually whichever file extension, I just use txt as it’s easiest to handle.

    Thanks again!

    Like

  3. Dysa Limitares says:

    How to put boostrap values using menu interface? Will you please help me? Thanks.

    Like

    1. Penny says:

      You know what’s really sad is that TNT was updated after I wrote this (and I don’t have a Mac), and now none of the things that used to work seem to work any more. I don’t know that I can help you.. Sorry.

      Like

  4. JP says:

    Thank you! It is very informative to get started! Do you know of a list of the functions with their description so we could explore the software?

    Thank you again!

    Like

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