I was able to finish a Philip neighbor joining distance tree, but when I try the same dataset using PhyML and MrBayes they both fail because "Can not use PhyML Maximum Likelihood tool or the MrBayes tool.  ERROR 13:23 and ERROR 13:25
>has active key-value observers (KVO)!  These will stop working now that the window is recreated, and will result in exceptions when the observers are removed.Break in QCocoaWindow::recreate WindowIfNeeded to debug

I have UGENE v41.0 64 bit version Dec 3 2021
on a MacBook Pro running MacOS vVentura 13.4

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Hello,

First of all, these two errors ("Can not use PhyML Maximum Likelihood/MrBayes tool" and "has active key-value observers (KVO)!") are not connected to each other. The second error relates to Qt and doesn't affect anything in our case. We will fix problem as soon as we can, for now just try not to pay attention on it.

Now, we need to figure out, why don't phylogenetic tools work. For now, the log info is pretty cut and I can't figure the problem out. Please, process the following steps:

1. Click "Unipro UGENE -> Preferences...".
2. Go to the "Logging" tab.
3. Enable all log info (TRACE, DETAILS, INFO and ERRORS).
4. Check "Save output to file" and choose file you want to save log information to.
5. Click OK.
6. Repeat all steps you did.
7. After you received the same result, send us the "log" file.

I will tell you more about your problem and how to resolve it after I get the log file.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.