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ProPIP adjusting branch lengths even when told not to optimise them #2

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junniest opened this issue Jun 29, 2021 · 0 comments
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@junniest
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ProPIP adjusts branch lengths despite the configs saying it should ignore branch lengths. A snippet of the config file below:

optimization=ND-BFGS(derivatives=Brent)
optimization.reparametrization=false
optimization.max_number_f_eval=100
optimization.tolerance=0.00001
optimization.final=none
optimization.ignore_parameters=BrLen
optimization.topology=false
optimisation.alignment=false

In this case ProPIP should have optimised the substitution model parameters only.

Full config file and data:
data+config.zip

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