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.
Gitea/Forgejo's [[page|label]] shortlink is post-processed on rendered HTML
text nodes: it cannot match when the label contains inline formatting (a
code span splits the surrounding text into separate DOM nodes), and even
plain labels had target/text swapped from the intended order. Native
Markdown links are real AST link nodes and have neither problem.
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`.
Add documentation and define core tool constraints
Enhance the sidebar with navigation links and a Theory section. Introduce the Home file detailing the tool's functionality, including kmer size constraints, indexing architecture using super-kmers, supported input formats, and API subcommands.
Eric Coissac