"ugene.exe" on Windows and launching of MUSCLE or Kalign

A user reported that MUSCLE and Kalign can't be used for aligning sequences in the Alignment Editor.

During the problem investigation it was found that besides "ugenecl.exe" file there is also "ugene.exe" file. Note that the latter one mustn't exist on Windows. MUSCLE and Kalign were launched with "ugene.exe" instead of "ugenecl.exe".

Note that the UGENE instance was installed using the online installer (there was "setup.exe" file). The problem might have happened because of the version update, as "ugene.exe" had version 1.32, but the version of other files was 33.

It is required to:

• launch "ugenecl.exe" on Windows when MUSCLE or Kalign are called even if "ugene.exe" is present
• try to find out how "ugene.exe" appeared in the installation folder on Windows