How to use scripts to calculate CI, RI, and Bremer support values in TNT

[王吉申]

Hi every one. I'm using TNT to calculate the CI and RI numbers and Bremer support values. I have the scripts files named Bremer.run and Stats.run, but I have no idea how to use them.

[Emanuel Tschopp]

Hi,

if you have the input file of the matrix in the same folder as the TNT.exe file and the scripts, you can just write the name of the script in the command line after you ran the analysis, and it should work (normally...)

I hope this helps,

Emanuel

[王吉申]

Thank you very much. It worked!

Emanuel Tschopp於 2017年5月2日星期二 UTC+8下午11時55分34秒寫道：

[Crystal Klem]

Hello,

When I enter bremer.run in the command line, I get two warning messages. The first one says "Trees not fulfilling constraints will be discarded. Continue?", and when I press yes, the second warning message pops up: "Non-binary starting trees will be dichotomized (randomly). Continue?". When I press yes again, the first warning message pops up, and this continues indefinitely. If at any point I press no, a blank error message pops up and the whole process fails. Any help you can give would be appreciated!

Thanks,

Crystal

[王吉申]

Sorry for the delay. I went to Indonesia during the past 20 days....just back home. I will go out tomorrow to collect specimens again, maybe in one month.....I haven't encounter this problem you mentioned yet. How did you run the tree analysis before you do the commands? Maybe something went wrong in your analysis process?

Yours, Jishen Wang

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[Crystal Klem]

Hi,

Sorry for the delay on my side as well. First I load the input file, specify an outgroup, run a traditional search, and run a consensus search and save the trees to RAM. All of that goes smoothly. Then to calculate bremer supports I type "bremer.run" in the command line bar at the bottom. This causes a dialogue box to open with parameters, which I leave the same, and then I click OK. That is when I see the two error messages. Have you experienced anything like this before?

Thanks,

Crystal