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In this report, we describe an algorithm for a k-deep annotated prefix tree. The algorithm provides an alignment-free method for comparing nucleotide sequences in a computationally efficient manner. Differences in genomic sequences are measured by recording and comparing counts of words of length k or less in each sequence using the algorithm. Tree nodes are annotated with lists to store the number of times each word occurs in each of a group of sequences. Count differences among multipledoi:10.1145/1854776.1854792 dblp:conf/bcb/BrelandSNH10 fatcat:ud7crkb7zfg2rm7awgbitvlftq