metaWEPP enhances metagenomic analysis by extending resolution from species-level profiles to near-haplotype detection in complex sequencing datasets. It integrates taxonomic classification with phylogenetic read placement on species-specific mutation-annotated trees to select the haplotypes that best explain each sample, while also reporting unaccounted alleles indicative of novel variants. These results can be further explored through an interactive dashboard that provides detailed, read-level visualization for each species.