MEGAN allows you to specify magnitudes to reads.
To do so, please put an expression of the following format into the header line of each read:
magnitude=55
or
magnitude|55
or
weight=55
or
weight|55
to set a magnitude of 55
This feature is currently not implemented for import or meganization of DAA files.
By default, parsing of magnitudes is turned off. Enable it on the first tab of the Import from Blast dialog