Additional file 3 of Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria)

Additional file 3: Eimeria taxonomic annotation to species level based on phylogenetic analysis. A phylogenetic tree was produced for all Eimeria ASVs from each amplicon (10 amplicons targeting the 18S rRNA gene), reference sequences for Eimeria spp of house mice and other rodents. Bootstrap_MRCA_clade: Bootstrap values from the clade of each species (reference species sharing the most recent common ancestor) retrieved from the respective amplicon phylogenetic tree.