Figure 3. Building phylogenies from parasite reads for study of prospecting for zoonotic pathogens by using targeted DNA enrichment. A) After read classification, we extracted all the reads associated with a pathogen group. B) Those reads were assembled into contigs with a genome assembler. C) Simultaneously, we identified and extracted the target loci from all members of the pathogen group with available reference genomes to ensure that our final phylogeny has representatives from as many members of the pathogen group as possible. D, E) For each targeted locus, we combined the assembled contigs (D) and genome extracted loci for (E) multiple sequence alignment and trimming. F, G) Each aligned and trimmed locus is concatenated together (F) for phylogenetic analyses (G). H) If necessary, those steps are repeated for reads classified in other pathogen groups. Ref, reference; Sp, specimen.