Parsimony analysis in TNT using the command line version by Alexander Schmidt-Lebuhn.TNT Google Group: !forum/tnt-tree-analysis-using-new-technology."TNT, a free program for phylogenetic analysis." Cladistics, 24(5), 774-786, October 2008. Goloboff paper: PA Goloboff, JS Farris, KC Nixon (2008).Wayback Machine partial archive of TNTwiki.Remember, if you post scripts, (a) other people might use them and cite you, and (b) more importantly, you will be able to find it yourself when you've moved computers 5 years from now.) This wiki is hosted by wikidot, a major wiki server, and it is a free Educational-Resource account, so it should be pretty permanent. (Please send me scripts if you find missing ones, or if you have new ones you would like to archive. I am attempting to repair this in TNT scripts, below. Many of them were used in publications that referred to TNTwiki as the permanent archive. Feel free to add to it (you may have to email me to get access to PhyloWiki).Īnother problem was the loss of many of the TNT scripts found in the TNT script archive. I will attempt to re-create the basics of the help at TNTwiki. This is something of a crisis for anyone less than an expert user, as the TNT command structure is very obscure, and the wiki was almost the only online help. Unfortunately, TNTwiki - the old help wiki ( original / Wayback Machine partial archive) - has apparently permanently died. And, parsimony is an important way to "look at what the character data are doing", which is easily lost in complex Bayesian analyses. Examples include: finding coding mistakes, finding starting trees, and finding parts of the tree with no morphological support at all. Although I am really a Bayesian, when working with morphology datasets and their various coding issues, it can be extremely useful to quickly estimate parsimony trees. It will include basic functions for reading/writing data and trees from R to TNT, and parsing the TNT outputs. I ( Nick Matzke) am currently working on an R package I am calling TNTR. It is a parsimony phylogenetics program that allows very fast searches of huge numbers of cladograms. TNT stands for "Tree Analysis Using New Technology".
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