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v0.49.0

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@AADavin AADavin released this 16 Sep 11:10
· 61 commits to main since this release

Added

  • The substitution rate can vary among gene families:
    substitution=PerSite(1.0).varying_among('families', LogNormal(0.0, 0.8)) draws one multiplier per
    family before any site evolves, and the family keeps that value for its whole life. It multiplies
    the lineage clock rather than replacing it, so a branch of a gene tree is
    substitution × Δt × lineage clock × family multiplier substitutions per site. The multipliers are
    written in the sequence run's own family_multipliers.tsv, with a substitution column, and are
    .family_multipliers in Python; runs with parallel= or stream_to= write the file too. A
    nucleotide sequence run refuses the draw, because it evolves blocks rather than gene families. (#444)