UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:

• Embedded tool: the tool is integrated into the UGENE source code. Such tools are always available in UGENE independently on the UGENE package type. 
• External tool: the tool executable file (or files) is provided with UGENE. It is launched when one uses the tool in the UGENE GUI. The result is also shown in the UGENE GUI. Thus, the tool should be downloaded and specified in the UGENE Application Setting.