External Tools¶

The External Tools plugin allows one to launch an external tool from UGENE.

The folllowing tools are supported:

• Bowtie
• BLAST/BLAST+
• BWA
• CAP3
• ClustalW
• MAFFT
• MrBayes
• T-Coffee

To use an external tool from UGENE, the tool needs to be installed on the system and the path to it should be properly configured. However, there is no need in the additional configuration, if you’ve installed the UGENE Full Package, as it already contains all the tools by default.

Otherwise, if you’ve installed the UGENE Standard Package, you would need to configure an external tool in order to use it. Note that in this case you can download the package with all the external tools from this page.

To learn how to configure an external tool, read below.

Configuring External Tool¶

To configure an external tool:

1. Make sure the tool is installed on your system.
2. Set a path to the tool executable file in UGENE. It can be set on the External Tools tab of the Application Settings dialog.

If the path hasn’t been set for a tool, UGENE menu items that launch the tool are displayed in italic. For example, on the image below a path for the ClustalW external tool has been set, and paths for MAFFT and T-Coffee has not: