Introduces session persistence via the `--session` option, allowing sampled sets to be restored. Implements chunked dumps and shared checkpointing for alignment and tally artifacts, ensuring state restoration upon interruption. Refines sampling logic and introduces serialization mechanisms for state management.
This change implements a robust session management system allowing users to persist distance calculation samples and parameters across invocations. It includes concurrency-safe directory locking, deterministic parameter encoding, artifact integrity checks, and caching mechanisms to skip resampling when valid data is available.
Ensures that combined distance matrix calculations use the exact same site selection by retaining sampled data within Sankoff bundles. This involves refactoring post-sampling logic into shared functions, implementing `SankoffBundle` to reuse internal tally data, and adding validation to guarantee consistent site selection across all distance calculation paths.
Introduces support for rate heterogeneity via a Poisson-Gamma mixture model. This includes new command-line options (`--gamma-shape`, `--gamma-shape auto`) to enable automatic estimation of the shape parameter $\alpha$ based on substitution counts across partitions. The correction is applied to the distance metric, with logic to disable the correction if variance checks fail.
The `obikmer select` CLI no longer supports in-place index rewriting; the `--output` flag is now required, with benchmarks updated to use temporary directories for atomic replacement. Added `--dense` and `--force-copy` flags. Introduced `batch_presence_counts` to compute presence counts across multiple column groups in a single pass, eliminating redundant I/O. Refactored the aggregation pipeline to branch on layer content, applying the optimized batched counting for `Presence` layers. Enhanced the NUMA runner to catch worker panics, track them, and re-raise after thread join to prevent indefinite blocking.
Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
Introduce a new `Sparse` format alongside existing `Columnar` and `Packed` variants, enabling optimized row-major pairwise counting for distance and similarity metrics via the `CountPartials` trait. Update storage detection priorities, extend matrix dispatch logic to sparse backends, and correct diagonal/off-diagonal formulas in bit matrix partial computations. Expand layer APIs with format-agnostic `nonzero_iter`, update usage documentation for the `--sparse` flag, and add comprehensive tests verifying roundtrip integrity and metric equivalence against dense implementations.
Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.
Restructure the output files section into categorized subsections with tables. Add explicit mappings between command-line options and generated files. Define CSV matrix conventions, clarify mathematical formulas for distance calculations, and document execution commands for external phylogenetic tools.
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.
Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
Eric Coissac