Benchmarking of alignment-free sequence comparison methods

Genome Biol. 2019 Jul 25;20(1):144. doi: 10.1186/s13059-019-1755-7.


Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.

Results: Here, we present a community resource ( to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events.

Conclusion: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

Keywords: Alignment-free; Benchmark; Horizontal gene transfer; Sequence comparison; Web service; Whole-genome phylogeny.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Benchmarking
  • Gene Transfer, Horizontal
  • Internet
  • Phylogeny
  • Regulatory Sequences, Nucleic Acid
  • Sequence Alignment
  • Sequence Analysis*
  • Sequence Analysis, Protein
  • Software