T N T
TNT stands for "Tree analysis using New Technology". It is a program for phylogenetic analysis under parsimony (with very fast tree-searching algorithms; Nixon, 1999, Cladistics 15:407-406; Goloboff, 1999, Cladistics 15:407-428), as well as extensive tree handling and diagnosis capabilities. It is a joint project by Pablo Goloboff, James Farris, and Kevin Nixon.
As of November 2007, the project was subsidized by the Willi Hennig Society, and thus the program is now made freely available, upon agreement on the terms of the license presented by TNT when it is run for the first time in a machine (a copy of the license can be found here). The license provided is a single-user license, and the most important requirements are that the program is not posted in other websites or mirrors, and that when publishing results you acknowledge having used the Willi Hennig Society edition of TNT and cite the paper describing the program (Goloboff et. al, 2008, in Cladistics)
Note for running TNT in parallel, under Linux or Mac.- You have to install PVM in your machine, and copy the binary file to the PVM directory for binaries (either to $PVM_ROOT/bin/LINUX, or LINUX64, or DARWIN). Mixing 32 and 64 bit versions poses no problem, but binaries with limits on number of taxa do not connect properly to binaries without such limit, and viceversa. To avoid mixing, you can rename the binaries of any type (and make sure you copy identically renamed binaries to the corresponding PVM directory). You should no longer have problems compiling PVM, if you download a recent version (previous versions had problems with some compilers, but they have been fixed now --thanks, PVM guys!!). Note on PVM and Mac 64.- The makefile provided with the PVM package does not explicitly specify the -m64 switch (which, in at least some compilers/installations, is not the default, even in 64 bit machines). The 32-bit daemon communicates correctly with TNT, but if you want to use PVM to transfer a LOT of data, having a 64-bit daemon may be good to let it access more memory. If you want to compile PVM for 64-bits, copy this makefile to your $PVM_ROOT directory, then type "make clean" followed by "make install".
Updates.- Updates are done regularly (often every 2 months or so). The last update was done on May 8, 2013. Note that the Mac PPC version is no longer maintained (last version is of December 2007). A list of recent additions and bugfixes is maintained here.
(for new or lazy users)
A simple, one-shot analysis is now included in the "aquickie.run" script, which comes with all TNT versions. This runs a simple analysis with a search for most parsimonious trees (or asks whether you want to do a consensus estimation, if the data set is large), then calculates group supports using resampling.
Windows.- To run this under Windows, you first open your data set, and then open "aquickie.run". Alternatively, to run data in file "filename.tnt" open a DOS shell, and type:
tnt filename.tnt ; aquickie ; [enter]
Linux/Mac.- You have to open the data file yourself, and then run the script. To do this, enter TNT and then type at the command line:
proc filename.tnt ; aquickie ; [enter]
The script will provide you with a few choices, then run the analysis automatically.
The GB>TNT program (or GB2TNT, by Goloboff & Catalano) provides an easy way to create data sets for TNT from GenBank data (including all the taxonomic information from the GenBank files, so that it is easy to diagnose results and color different taxonomic groups). The program and documentation (still in beta; current version is 0.75) is included in the package for all Windows versions; you can also download it separately.
The main documentation is in the file tnt.htm, and recent additions or bugfixes are in the file BugFixes.htm; both of these are contained within all the packages (except the character-mode Windows version). On-line help on all TNT commands can be obtained with the help command. A general description of the Windows version is in a QuickTutorial (a PowerPoint presentation; this is probably the easiest way to get started). The example files for scripting come in the self-extracting files zipdruns.zip or tnt_scripts.zip, and additional scripts (with full documentation in a pdf file) are here. Finally, a TNT wiki has been created recently, with some additional info. Instructions to view large trees in Windows and process the taxonomy contained within taxon names (as in Goloboff et al., 2009, Cladistics 25:211-230) can be found here.
Keep in mind that freezes/crashes might occassionally occur, and save results frequently. The program is intended only for strictly academic use, and is provided "as is," with no express or implied warranties. None of the authors of TNT is responsible in any way for any problems the program causes to your computer, your data, your career, or your life. A copy of the license agreement can be found here.
Bug reports are appreciated, but please keep in mind that a bug report, to be of any use, must include the version of TNT (including date), the complete data file, and all the commands necessary to show the bug (or, at least, the exact sequence of menu operations that consistently leads to a crash, freeze, or miscalculation). Send bug reports to Pablo (firstname.lastname@example.org), with "tnt bug report" in the subject.
To properly view the trees drawn by TNT with extended ASCII characters you will need
to install the Tred.ttf font (available here).
In Windows, you can just copy it to the Fonts directory (or
install from control panel). In Linux or Mac, you will have to copy
Tred.ttf to the directory where other True Type fonts (*.ttf)
are located (probably something like /usr/X11R6/lib/X11/fonts/TTF/ in
Mac, or /usr/share/fonts/truetype/ in Linux). The second step you
need to do, for each file to view, is to convert it to unicode
characters, using the converter to unicode, tounicode
(available for Mac
32, and Linux
tnt_output_file unicode_file <enter>
tounicode tnt_output_file unicode_file <enter>
Then, you can open unicode_file with Open Office, or the like, select all text, and change font to Tred. The trees will then look ok.