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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
