I used Recreated SEED database for allignment and greengenes ref taxonomy for classification. I se that many of the genus has more than one parent. For exmple-
a) k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Macellibacteroides s__fermentans
b) k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Marinilabiaceae g__Cytophaga s__fermentans
This disturbs formation of a strict hierarchy. why is this so ?
Which step should I concentrate to solve this?
Second question, I a couple of the classified species had unclassified parent in my output taxonomy file. why ?