Help! Running phylogenetic analyses in TNT

I’ve got a problem. For a paper I’m working on, I need to run a phylogenetic analysis based on that of Mannion et al. (2013) — the Lusotitan paper. The most recent version of that matrix, greatly expanded from the original version, is that of Mannion et al. (2019) — the Jiangshanosaurus paper — so I am working from that matrix.

But what exactly do I do with that Matrix? The analysis protocol is described on pages 12-13 of the PDF:

Several unstable and fragmentary taxa were excluded from the analyses (Astrophocaudia, Australodocus, Brontomerus, Fukuititan, Fusuisaurus, Liubangosaurus, Malarguesaurus, Mongolosaurus). Using equal weighting of characters, this pruned data matrix was analysed using the ‘Stabilize Consensus’ option in the ‘New Technology Search’ in TNT v. 1.5. Searches employed sectorial searches, drift and tree fusing, with the consensus stabilized five times, prior to using the resultant trees as the starting topologies for a ‘Traditional Search’, using Tree Bisection-Reconstruction. We then re-ran the analysis, using the same pruned matrix and protocol, but also applying extended implied weighting in TNT.

There is no problem downloading TNT: it’s freely available thanks to subsidy by the Willi Hennig Society. But the program is tricky to use, and documentation is rather cryptic. You drive TNT with scripts that look like this (short excerpt):

ttags =;

ttags );
tsave *tags.tre;
save *
;
tsave /;

It seems, for example that = and ) are values that the ttags command accepts. But I’ve not been able to find documentation that spells out such things. (There is a help command, but its output too is cryptic.)

So here is my problem: how do I translate the Mannion et al. (2019) protocol into a TNT script? If anyone can help me with this, I will acknowledge the heck out of them the paper that eventually emerges from this rubble.

(Why not just ask Phil Mannion, you ask? I’ve been talking with Phil and he has been super-helpful: but he’s been using a Windows-only version of TNT in which you don’t write scripts, but invoke various menu options, so he’s not able to help with this directly.)

Thank you!

References

• Mannion, Philip D., Paul Upchurch, Rosie N. Barnes and Octávio Mateus. 2013. Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms. Zoological Journal of the Linnean Society 168(1):98–206. doi:10.1111/zoj.12029
• Mannion, Philip D., Paul Upchurch, Xingsheng Jin and Wenjie Zheng. 2019. New information on the Cretaceous sauropod dinosaurs of Zhejiang Province, China: impact on Laurasian titanosauriform phylogeny and biogeography. Royal Society Open Science 6:191057. doi:10.1098/rsos.191057