Version

TNT version and version 1.1 (July 2007) in Hippu and Murska.

Description

TNT is a very fast program for the inference of phylogenies with parsimony method.

Usage

For TNT a NEXUS-formatted sequence alignment file is needed.

On Hippu, the program is started with the command tnt.  On Murska user should type the command /v/linux26_x86_64/appl/molbio/tnt/tnt-init.sh in the home directory before using the program.
After initialization the program can be run using a command tnt. Commands are types in the program's own prompt (tnt*>).

A simple analysis using TNT could proceed as follows. Note the placing of semicolons!

1. Read in the data: p rat1.nxs
2. Switch taxon names ON: taxname =
3. Set outgroup taxon: out 12
4. Hold a maximum of 100 trees in memory: hold 100
5. Tree search using 100 RAS and TBR: mult=tbr replic 100 hold 1;
6. Display tree lengths: length;
7. Save the trees in parenthetical format: tsave *trees.out; save; tsave /;
8. Resampling using jackknifing: resample=jak probability 34 frequency;
9. Quitting the program: quit;

Manual

The manual gives background to the implementation features. A detailed description of TNT commands is found in the command manual. TNT also comes with a built-in help. You can get help for individual commands by typing, e.g., help procedure (help and the name of the command).

Manuals for Hennig86 and Paup* might be of use, also.

You might also want to read the worked-out examples in Molecular systematics - material for practicals".

Distribution

TNT can be downloaded and purchased from it's website.

User support