multiple B cell epitope prediction with IEDB

Question

[BCArg]

Dear all,

I've downloaded the free command line version of the IEDB software to predict B cell epitopes. Does anyone know whether is it possible to run multiple proteins from a single file? I tried to do that and firstly it complained about the ">" from the headers. So I removed them such that the proteins were separated by an empty line (enter). But then the program considered my proteins as a single one.

Does anyone know how to get around that?

Thanks and best regards