All,
I taught myself how to use TNT so I may be using it in a different way than yourself – I do not use commands in the command line, I use the mouse and a computer with Windows. I would like to explain how I am getting my MPTs and if you may, please let me know what you are doing differently. The point of this activity is determining the relationships of the ingroup taxa via the creation of a strict consensus. I am using a morphological dataset and my matrix includes 112 taxa, 171 characters, 16 states. Below are the steps I am using to get the MPTs from TNT.
I load the .ss file into TNT, select 1000 megabytes of RAM and set the max trees as 99,999 which is as many as the interface allows when not using the hold function in the command line. I do not use collapsing rules.
Next I select a traditional search. 1000 replicates for this example, saving 10 trees per replicate and using the TBR swapping algorithm.
Then I run the search and get 620 trees, but some have overflowed.
Because there was an overflow of replications I re-run the analysis on the trees stored in RAM.
During the second round of TBR I get the max number of trees I selected in the beginning, if I set max trees to 10,000 then it returns that many, if max trees set to 99,999 then I get that many. This is where my confusion lies – I’ve looked at many references and cannot solve this issue. A third round of TBR produces the max number of trees selected in the beginning (99,999).
Any help is appreciated! --- Adam
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