Hello, AK.
There are 2 different problems with your UGENE installation:
1. When you open a Build Tree dialog, it is almost empty and there is a error in log "PhyTree Generator is NULL". We've got to reproduce it and it will be fixed in the upcoming UGENE 1.21. Follow the progress
here.
2. MrBayes and PhyML don't work, they finish with an error.
How to fix problem 1:As I understood you have installed UGENE from
PPA. Am I right? If yes, it will be better if you install the non-free UGENE plugins (PLHYLIP is one of them) with the following command:
sudo apt-get install ugene-non-free
PHYLIP is distributed with another license that's why it is not included into the main UGENE package.
How to fix problem 2:I can't answer it now, because I can't reproduce it. Could you help me with it?
Currently I need to know what MrBayes and PhyML versions you use. You can check it in UGENE:
a. Click the menu Settings -> Preferences.
b. Click the "External Tools" section.
c. Find MrBayes and click it.
d. Check its version in the additional information block.
Repeat c and d for PhyML.
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