I downloaded uGENE v.1.6.0 to my Mac (Intel MacPro tower, 2x3 GHz Dual-Core Xeon, 8 GB 667 MHz DDR2 FB-DIMM, OS X, 10.5.8). I had no trouble running the main program, but discovered that no plugins had been added. The directory /usr/lib/ugene/plugin was never made. I created it from Terminal.app, and reinstalled uGENE, but again, no plugins were installed. This greatly limits the utility of the program. Can anyone tell me what I'm doing wrong?

I discovered that plugins on the Mac are at /Applications/Unipro UGENE.app/Contents/MacOS/plugins/ rather than /usr/lib/ugene/plugins, and that all are loaded at run time. So, how do I do a multiple sequence alignment with MUSCLE? My menu bar has only "Files", "Settings", "Tools", "Window", and "Help". I can't find anything under any of them which relates to multiple alignment or multiple sequence editing. At the uGENE web site, the illustrations all show an "Actions" menu, but this is missing from my setup. This is getting frustrating...

eckofoid wrote on Jan 29^th, 2010 at 6:39am:

So, how do I do a multiple sequence alignment with MUSCLE? My menu bar has only "Files", "Settings", "Tools", "Window", and "Help". I can't find anything under any of them which relates to multiple alignment or multiple sequence editing. At the uGENE web site, the illustrations all show an "Actions" menu, but this is missing from my setup. This is getting frustrating...

To get the actions menu you need some documents to be opened
Click File->Open and select the file with alignment. Once it opened you'll see the alignment editor and will have access to the action menu.
Note that you'll see 2 options: 'Muscle' and 'Muscle4' for the alignment. 'Muscle4' is an experimental code now, so I propose using 'Muscle' option.

eckofoid wrote on Jan 29^th, 2010 at 6:39am:

I discovered that plugins on the Mac are at /Applications/Unipro UGENE.app/Contents/MacOS/plugins/ rather than /usr/lib/ugene/plugins, and that all are loaded at run time. So, how do I do a multiple sequence alignment with MUSCLE? My menu bar has only "Files", "Settings", "Tools", "Window", and "Help". I can't find anything under any of them which relates to multiple alignment or multiple sequence editing. At the uGENE web site, the illustrations all show an "Actions" menu, but this is missing from my setup. This is getting frustrating...

This post might be helpful for you:
http://ugene.unipro.ru/forum/YaBB.pl?num=1259091467