TY - JOUR AU - Zielezinski, Andrzej AU - Vinga, Susana AU - Almeida, Jonas AU - Karlowski, Wojciech M. PY - 2017 DA - 2017/10/03 TI - Alignment-free sequence comparison: benefits, applications, and tools JO - Genome Biology SP - 186 VL - 18 IS - 1 AB - 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. SN - 1474-760X UR - https://doi.org/10.1186/s13059-017-1319-7 DO - 10.1186/s13059-017-1319-7 ID - Zielezinski2017 ER -