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armanbilge / B3

Bayesian Evolutionary Analysis by Sampling Trees
GNU General Public License v3.0
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Merge beast.evomodel and beast.beagle #8

Open armanbilge opened 9 years ago

armanbilge commented 9 years ago

It seems very redundant to have separate evomodel interfaces/implementations for Beagle.

In fact, I see that the Beagle Jar has its own pure-Java implementation. This means that we should be able to remove the BEAST implementations and rely entirely on Beagle, regardless of whether it is actually installed on the system.

armanbilge commented 9 years ago

After speaking with @alexeid today I learned that the highly-optimized Beagle implementation may return values that are inconsistent with various reference implementations (such as the BEAST implementations). Therefore it is valuable to keep the BEAST implementations, although I hope it is still possible to merge these packages at least to some extent.