Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

By Gregory E. Sims, Se-Ran Jun, G. Wu, Sung-Hou Kim. Proceedings of the National Academy of Sciences of the United States of America, 2009

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Alignment-free sequence comparison: benefits, applications, and tools (2017, background): “As a rule of thumb, smaller k -mers should be used when sequences are obviously different (e.g., they are not related) whereas longer k -mers can be used for very similar sequences [55, 58].”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “Alternative approaches to analysing protein-coding genome data (e.g. nucleotide-based analyses) or using alignmentfree genome similarity methods (Sims et al., 2008), or approaches that target different types of data (e.g. genome skimming, targeted enrichment, ultraconserved elements: Faircloth et…”