Multiple parent to a common species_why ?

Hello everyone,

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 ?

I se that many of the genus has more than one parent

You mean there are species with different genera? I suspect fermentans is a pretty generic name that has been reused. For example, “coli” does not necessarily mean that it is from Escherichia coli (see Entamoeba coli).

classified species had unclassified parent in my output taxonomy file.

Probably because that lineage does not have well-defined taxonomic levels. For example the TM7, Acidobacteria, etc. may not have defined classes, orders, and families.