TNT and Ubuntu

TNT (or ‘Tree analysis using New Technology’) is a relatively fast parsimony-based phylogenetics program. However, to be quite frank, it is also totally confusing. It took me some time, but I have put together a script that does pretty much everything I want it to do now, so I can just reuse the script every time I need to do something. I’m posting it here, in the hopes that other people will not have to spend so long figuring this all out. Just note though, the actual commands are in this type of font.Of course, everything that follows is what I’ve figured out through reading papers and trawling the internet, so suggestions are appreciated.

First things first, make sure your data is in the correct format. Theoretically, TNT can handle .nex files, but then again, my old car could theoretically do 220 km/h because the speedometer went that high. Your best bet is to just take your .nex file and reformat it to .tnt format, which pretty much involves deleting everything except the actual matrix, and then editing the first few lines. The first line should read ‘xread’, with the next line containing the number of characters, a space, and the number of taxa. (You can add a line between those for a comment, just be sure to put the comment in quotes)

For example, a simple data set might look like this:

xread
‘sample phylogeny’
5 3
taxonA 00011
taxonB 01111
taxonC 11111
;

While TNT is not the most user-friendly program, using scripts can help a lot, as you often will run the same set of analyses on different data sets. For my purposes, most of the time I want to run a basic tree search to find all of the most parsimonious trees, find a consensus tree from that (if necessary), map the characters, get bootstrap values and finally find the Bremer supports. At the bottom of the page I’ve posted my default TNT script that I use. Note that it does include comments (lines with a # in front) that will need to be deleted for the script to run properly. Also, replace ‘samplephylo’ with whatever you’ve named your .tnt file. Finally, when you’ve done all that, you need to move both the script and the .tnt file into the folder that contains all the files for the TNT program (on mine, the folder is called ‘tnt64-no-tax-limit’).

Finally, once you’ve done all that, you can run TNT (usually by navigating in a terminal to that same ‘tnt64-no-tax-limit’ using the change directory command [i.e. cd]), and then running TNT by typing something like ‘sudo ./tnt’. Note that TNT typically doesn’t run properly unless you run it as root/administrator (same applies to Mac OS X, except you’d run it as ‘sudo ./tnt.command’).

Often, TNT will throw error messages for no apparent reason. A few things to make sure of is that all the file names are letters or numbers only (no punctuation, including periods or underscores, and no spaces), that both the command script and .tnt file are in the same folder as the TNT program and that the program is being run as root/administrator. Hopefully by putting this up here, more people will be able to finally figure out how to use TNT.

#take everything after here and put it in a file in the tnt folder
#delete all the lines that start with the # sign
#replace the ‘samplephylo’ with the name of your file. I recommend converting
#your matrix to .tnt format, which is pretty simple
#check out the example.tnt file in the tnt folder to see how it’s done
#the most imprtant part is the first few lines,
#but be sure to convert any polymorphisms to [] brackets
#load the data file
procedure samplephylo.tnt;
#write all the output to this file
log samplephylo.out;
#do a basic run – finds a bunch of parsimonious trees quickly
mult ;
#this should find all the MPRs
bbreak=tbr;
#find the consensus tree
nelsen * ;
#map the synapomorphies on the tree
apo [ ;
#export the MPRs and the consensus tree to a file
export samplephylo.tre;
#do a bootstrap analysis – might need to up the runs
resample ;
#the stuff below does a Bremer analysis
#it’s a bit convoluted, but is the only way to get
#TNT to do a Bremer, because TNT isn’t really meant to
#do a Bremer analysis
hold 1000; sub 1 ; bbreak=tbr;
hold 2000; sub 2 ; bbreak=tbr;
hold 3000; sub 3 ; bbreak=tbr;
hold 4000; sub 4 ; bbreak=tbr;
hold 5000; sub 5 ; bbreak=tbr;
hold 6000; sub 6 ; bbreak=tbr;
hold 7000; sub 7 ; bbreak=tbr;
hold 8000; sub 8 ; bbreak=tbr;
#calculate the Bremer support from the suboptimal trees
bsupport ;
#quit the program – you can always do this manually
quit