v0.0.5

• Fixed issue with missing packages during the Conda build process
• Added optional --pylogeny and --extracts-tracts options to the README

v0.0.4

• Phylogeny of recombinant tracts: new optional -phylogeny mode builds a tree of Ia/Ib tracts plus references to show which outbreaks each tract descends from.
• This lets you confirm real recombination: true recombinants have tracts that cluster with two different outbreaks, while “false” MDRF hits cluster within a single outbreak.
• Together with MDRF (-m / -MDRF) this provides a stricter, tree‑based check on recombination calls.
• Various bug fixes and easthetic improvements in html

v0.0.3

• Added option: -m/--minor-ref-pct to adjust the minor-reference % threshold for calling “potential recombinant”.
• Added option:: -b/--breakpoint-snp to ignore single-SNP tracts when inferring breakpoints (requires ≥2 consecutive diagnostic SNPs).

v0.0.2

• Field-tested in Kinshasa (DR Congo) during the ongoing Clade Ia/Ib outbreak [sh2024/sh2023] (functionality validated in real-world conditions).
• Disabled SSL verification to improve downloading of online accession numbers.

v0.0.1

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