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.
This commit introduces new constraints for kmer size and minimizer selection, defines super-kmers, and adds extensive new command-line options for filtering, conversion, merging, and packing indices. Documentation across the codebase has also been updated.
Update sidebar separators and refine SNP model definitions
Modifies list item formatting in the sidebar to use double pipe separators. Also updates mathematical definitions and parameter sets for several SNP models, including new parameters for `snp-tn93`.
Implement advanced indexing architecture and query features
Introduces a partitioned, NUMA-aware indexing system, supports kmer filtering, evidence conversion, index packing, and advanced query capabilities including estimation and phylogenetic analysis.
Eric Coissac