raxml returns higher likelihood for constrained tree than unconstrained tree for some simulated matrices

Question

raxml returns higher likelihood for constrained tree than unconstrained tree for some simulated matrices

Closed this issue 9 years ago · 2 comments

This is a known issue, and is addressed here:

https://groups.google.com/forum/#!topic/raxml/qn7_ZXoJTHg

We should redo some of hte problematic searches with the addition of the --no-bfgs raxml option. If that fixes the problem for those matrices, we should rerun the tests in the manuscript that were impacted by this. If they work, we should revise the manuscript to reflect the fix.

Answer 1 · 2015-05-09T17:01:32.000Z

Currently testing if removing BFGS protocol resolves the issue. Preliminary results indicate that yes. See https://groups.google.com/forum/#!topic/raxml/qn7_ZXoJTHg

Answer 2 · 2015-06-12T19:13:26.000Z

RAxML restored to default lieklihood engine.