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Updated: Feb 21, 2026

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Alignment-free sequence comparison: benefits, applications, and tools
Andrzej Zielezinski1, Susana Vinga2, Jonas Almeida3
1Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
Abstract:
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
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