The phylogenetic intersection analysis (PIA) is a method of metagenomic phylogenetic assignation that is designed to be robust to the uneven representation of organisms in databases. An early version was published in Smith et al. (2015) and an updated version in Cribdon et al. (2020).
Smith, O., Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, M., Gaffney, V., Allaby, R. G. (2015). Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, 347(6225). https://doi.org/10.1126/science.1261278.
Cribdon, B., Ware, R., Smith, O., Gaffney, V., Allaby, R. G. (2020). PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on SedaDNA From the North Sea. Frontiers in Ecology and Evolution, 8(84). https://doi.org/10.3389/fevo.2020.00084.