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.
Refactor Kmer indexing and add phylogenetic analysis features
This commit introduces a complete overhaul of the Kmer indexing architecture, including new support for 2-bit encoding, canonical super-kmer handling, and a partitioned processing pipeline. Additionally, it adds comprehensive phylogenetic capabilities, including multiple distance metrics, SNP correction models, and models for rate heterogeneity and sampling design.
Eric Coissac