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EukPhylo version 1.0 is an updated version of the PhyloToL pipeline from the Katz Lab (https://www.science.smith.edu/katz-lab/) at Smith College. EukPhylo is a phylogenomic toolkit for processing transcriptomic and genomic data that includes novel phylogeny-informed contamination removal techniques. See our Wiki (https://github.com/Katzlab/EukPhylo/wiki) for more information on installation and usage!