Greetings,

Can anyone help me with a bootstrap resampling problem in TNT?

I am currently running an analysis with TNT in a data matrix composed by morphological characters (105 discrete and 25 continuous characters) and 87 taxa. From previous tests on TNT, I reached the conclusion that my dataset is rather complex, thus searches with default parameters for both traditional and newtech search cannot find the best result. I have been using a script with the following commands for my searches:

keep 0 ;

ttags - ;

hold 99999;

rseed 1 ;

sect:slack 1000 ;

xmult= hit 3 level 7 rat 10 drift 10; bb;

HOWEVER, I have been finding problems to run bootstrap support for this dataset: I cannot finish running the analysis. The resampling always stops doing new replicates before reaching the 500 replicates I have set. The bootstrap running analysis window will stop updating altogether for hours, until I manually stop the analysis.

These are the commands I have been using for the bootstrap search:

keep 0 ;

ttags - ;

hold 99999;

rseed 1 ;

sect:slack 1000 ;

ttags = ;

resample boot replications 500 [xmult= hit 2 level 5 rat 10 drift 10; bb] frequency gc ;

I have tried changing the parameters for the bootstrap analysis and using the default parameters from TNT, BUT they either still cannot finish 500 replicates, or when they finish the bootstrap values are exceedingly low (most likely because the resampling is not managing to find topologies close to the optimal I have found with the search).

Would anyone have any tips on how to change the parameters and commands to finish the 500 (or even 1000) replicates I am trying to achieve, while managing to do a good enough resampling of my data?

If desired, I can e-mail the matrix I am using and both scripts.

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