Defines various distance metrics for k-mer sets, including presence/absence-based (Hamming), abundance-based (Euclidean), Hellinger, and Bray–Curtis dissimilarity.
Introduce k-mer based distances (Hamming and Mash).
Defines the Hamming distance based on k-mer presence/absence vectors and introduces the Mash distance, noting it is an evolutionary estimator rather than a metric.
Document the theoretical classification of k-mer set distances based on information retained and metric properties.
Defines new presence/absence and abundance-based distances, including Jaccard, Hamming, Euclidean, and Hellinger. Clarifies metric properties of various dissimilarity measures.
Refactor phylogenetic models and update usage documentation
This commit removes entries related to Kmer-based and SNP-based phylogenetic methods, refining the definitions for SNP models, and introducing new documentation for k-mer based set-based distances. Additionally, new configuration options and exclusion flags are added to clarify tree generation behavior.
Eric Coissac