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Curious HyPhy user
Posts: 7
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I am trying to partition my data so that I can assign different models to different sites. In effect, I change from
LikelihoodFunction likelihood = (allsitesfilter, allsitestree);
To instead use:
LikelihoodFunction likelihood = (filter1, tree1, filter2, tree2, ...)
Eventually, each tree (tree1, tree2, ...) would get a different model. However, the trees would all have their branch lengths constrained to be equal, so there are no additional parameters in the second case if all trees use the same model. For a sanity check, I first just tried doing this where each tree gets the same model. I believe in this case the same inference is being done in both cases.
However, the first case converges to a solution fairly quickly. But the second case is still running! Is there some reason the performance is so slow -- and if so, how do I speed it up?
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