Replaces external Python glue with native Rust modules for Sankoff model calibration, exporting calibrated cost matrices, FASTA alignments, and YAML parameters. Adds dedicated writers for TNT and PhyG that apply integer scaling and Floyd-Warshall metric closure to enforce triangle inequality. Integrates these exporters into the distance command pipeline to streamline downstream tree inference workflows, while updating theory documentation to reflect IQ-TREE integration and state renumbering improvements.
Eric Coissac
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