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
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 https://doi.org/10.1093/nar/gkx351
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 https://doi.org/10.1093/bioinformatics/btu028
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