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If you used PhyloPhlAn 1.0 and found it useful, please cite:
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes Nicola Segata, Daniela Börnigen, Xochitl C. Morgan, and Curtis Huttenhower
Nature Communications, vol. 4, p. 2304, Jul. 2013
DOI: 10.1038/ncomms3304