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After updating to phangorn 2.5.3, a codon tree with ~30 nodes that previously converged quickly with optim.pml(model="codon1",optBf=T,optNni=T) now iterates forever, without any (visible) changes in the likelihood. I've tried to reduce the number of nodes, but the problem persists, and if I remove the topology optimization it converges quickly.
After updating to phangorn 2.5.3, a codon tree with ~30 nodes that previously converged quickly with optim.pml(model="codon1",optBf=T,optNni=T) now iterates forever, without any (visible) changes in the likelihood. I've tried to reduce the number of nodes, but the problem persists, and if I remove the topology optimization it converges quickly.
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