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

Genome Biol. 2017 Oct 3;18(1):186. doi: 10.1186/s13059-017-1319-7.


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.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • High-Throughput Nucleotide Sequencing
  • Information Theory
  • Sequence Alignment
  • Sequence Analysis / methods*
  • Sequence Homology
  • Software