due to licensing restrictions on KEGG, MEGAN does not ship with KEGG pathways. (MEGAN5 contained pathways dating back to 2011, before KEGG licensing changed.)
However, if you have a KEGG ftp license, then the Ultimate Edition of MEGAN allows you to view KEGG pathways within MEGAN using files downloaded from KEGG. To achieve this, using your licensed access to the KEGG ftp site, In this case, using your licensed access to the KEGG ftp site, download the KEGG files to a local directory.
Assuming that MEGAN 6 Ultimate Edition is installed in ~/megan and you have downloaded KEGG to ~/kegg, to enable visualization of KEGG pathways in MEGAN6, do the following:
tar xzf ~/kegg/xml/kgml/metabolic/ko.tar.gz
tar xzf ~/kegg/xml/kgml/non-metabolic/ko.tar.gz
mv ko/* .
mv map/*.png .
cp ~/kegg/xml/kgml+/*.xml .
tar xzf ~/kegg/pathway/map.tar.gz
This will give MEGAN access to all required files.
Then restart MEGAN6 Ultimate Edition. If you did everything correctly, then MEGAN will report KEGG bundled detected - will be able to display KEGG pathways in the message window, and you will be able to view KEGG pathways in the KEGG Viewer.
I am currently updating the user manual to explain exactly how to fully update MEGAN's representation of KEGG if you have a KEGG ftp license.