I ran “blastn” against a custom reference of 16 genomes and loaded the output into MEGAN with the following parameters (that can also be seen at the bottom of the screenshot):
LCA algo: weighted
Percent to Cover: 80
As seen below, a read that was assigned to Linum also has matches aligning to Castanea, one of each even with a higher score than the top scored for Linum.
How can I improve the specificity of the LCA algo for these situations?
Thanks in advance,