I need some explanation. I have blasted some sequences and some how it looks like that MEGAN6 does not read the input file good. Here two screenshots, one of megan6 and the other one of the input. As you can see the identity’s are different. A “|” character indicates a match but in MEGAN6 it ignores some matches.
It is probaly the softmasking, how can I turn that off in MEGAN?