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CAFE is a software tool using alignment-free methods to compute distance or dissimilarity by k-mer counts, background-adjusted k-mer counts, or measure based on presence/absence of k-mers, and 25 additional measures. CAFE visualization includes heatmaps, two-dimensional projection by principal coordinate analysis (PCoA), dendrograms of a network, and sequence clustering by the neighbor-joining algorithm.


Metagenomics; Sequence assembly; Sequencing


  • Operation: Sequence assembly; k-mer counting; Sequence alignment
  • Software interface: Command-line interface, Graphical user interface
  • Language: Python;C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: USC-RL v1.0
  • Cost: Free
  • Version name: -
  • Credit: NSF; OCE; NIH; Gordon and Betty Moore Foundation Marine Microbiology Initiative.
  • Contact: ylu465 _at_;fsun _at_
  • Collection: -


Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F "CAFE: aCcelerated Alignment-FrEe sequence analysis." Nucleic Acids Res. 2017; 45(W1):W554-W559
PMID: 28472388
PMCID: PMC5793812

Bollen S, Leddin M, Andrade-Navarro MA, Mah N "CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data." Bioinformatics 2014; 30(10):1484-5
PMID: 24451624
PMCID: PMC4016701

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