So I’ve started working on a phylogenetic project, after a long break from anything directly working with them. As such, I find myself back at the beginning of having to learn how to do a few things again, in particular the powerful yet cryptic program known as TNT (“Tree analysis using New Technology”). To get TNT started on a Linux box, follow the steps below:
Step 1: Download TNT from http://www.lillo.org.ar/phylogeny/tnt/
Step 2: Save your matrix/nexus files into TNT format using some of the tips here: https://matthewvavrek.com/2011/10/19/tnt-and-ubuntu/
Step 3: Navigate to the TNT folder in a terminal, and then spend 10 minutes trying to figure out why TNT isn’t running when you type in “sudo ./tnt”
Step 4: Realise you wasted 10 minutes because all you had to do was make sure the “tnt” file (the one in the folder you downloaded) was made executable; do this by navigating in a terminal window to the TNT folder, then type in “sudo chmod +x tnt”.
Step 5: Sigh deeply, and come to the realization that using TNT again after not having touched it for 4 years is unlikely to be “phun” at any point.
Palaeontology 2.0 