We describe a new tool, KATKA, that stores a phylogenetic tree T such that later, given a pattern P [ 1 . . m ] and an integer k , it can quickly return the root of the smallest subtree of T containing all the genomes in which the k -mer P [ i . . i + k - 1 ] occurs, for 1 ≤ i ≤ m - k + 1 . This is similar to KRAKEN's functionality but with k given at query time instead of at construction time.
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