WEPP (Wastewater-Based Epidemiology using Phylogenetic Placements) is a pathogen-agnostic pipeline that enhances wastewater surveillance by leveraging the pathogen's full phylogeny. It reports haplotype and lineage abundances, maps reads parsimoniously to selected haplotypes, and flags Unaccounted Alleles — those observed in the sample but unexplained by selected haplotypes, potentially indicating novel variants. WEPP performs parsimonious read placement on the mutation-annotated tree (MAT) to select a subset of haplotypes and adds their neighbors to form an initial candidate pool, which is passed to a deconvolution algorithm to estimate their relative abundances. An interactive dashboard enables visualization of haplotypes in the global phylogenetic tree and read-level analysis.