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Migrate CCD to beast3
Add setParentProbabilityThreshold(t): skip expanding around a parent clade whose marginal probability is >= t, on the premise that a near-certain parent has no alternative resolution worth adding. Default POSITIVE_INFINITY keeps the full expansion. compute() populates the lazily-computed clade probabilities when the gate is active. Gate applies in both GRAPH_WIDE and CO_OCCURRING paths. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
use beast 2.8.0-beta7
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