By Peter Unmack
TNT can be a little confusing to use. The following provides minimal instructions for running a bootstrap analysis.
Open TNT, go settings>memory and make it 600mb and for trees say 10,000. Open your data file (a nexus file is fine). Set an outgroup, Data>outgroup taxon, then select one (you can only select one). Next go Trees>multiple tags>store tree tags. To set up the bootstrap run go Analyze>resampling Bootstrap, standard. Unclick frequency differences and click on absolute frequency right above it, set the number of reps and use a traditional search. I don't change any of the other options as they all seem quite appropriate.
To view the results once the search has completed go Trees>multiple tags>show/save tags
You can either print out the tree or to save it hit m, which will prompt you to save the file as an enhanced metafile. At that point you are done. Hit escape to get back to the main TNT interface. You can also save the file to a nexus tree file, however, I've never messed with this. This link had the options, but the links are currently broken and I couldn't find the correct link to update them! http://tnt.insectmuseum.org/index.php/Commands/export. The FAQ explains how to convert it to newick format too. http://tnt.insectmuseum.org/index.php/FAQ#How_can_I_export_trees_then_convert_them_to_Newick_format.3F
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