One way to use MEGAN is as a rapid alignment-based annotation tool. This is especially useful when analyzing long reads and contigs. MEGAN analyses all given DNA-to-protein alignments and maps the given reference sequences into different functional classification schemes such as InterPro families, KEGG KOs, eggNOG clusters, etc.
MEGAN (6.9.2) now allows you to export long reads and contigs as annotated sequences that can be viewer in the Artemis genome browser.
To use this feature, first load your FastA file of long reads or contigs into Artemis using File->Open in Artemis.
Then, in MEGAN select the nodes that you want to export in the taxonomy viewer or a functional viewer, or select long reads in the long read inspector and then use the File->Export Read Annotations in GFF Format menu item.
The dialog will allow you to export a single type of annotation, for example Taxonomic or InterPro2Go, say,
Use the dialog multiple types to generate individual files for each type of annotation that you want.
Finally, back in Artemis, use the File->Read an Entry menu item to read in each of the GFF files save from MEGAN.
GFF3 format is a simple text-based format that you can easily phrase yourself for other purposes.
This is what annotated reads look like in Artemis: