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