Alignment-free sequence comparison: benefits, applications, and tools

Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
2017 Genome Biology  
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
more » ... e for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
doi:10.1186/s13059-017-1319-7 pmid:28974235 pmcid:PMC5627421 fatcat:5s7yd22l7bbmpljqc7fj4cbifm