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Published 20 hours ago • verified publisher icon KlausVigo

NNI parallelization

Open teng-gao opened this issue 2 years ago • 2 comments

  • Parallelizing nni using mclapply
  • Removing tip label inside nnin so it doesn't have to be done in the loop in nni

teng-gao avatar May 03 '22 14:05 teng-gao

Hi Klaus,

I was implementing Scistree maximum likelihood phylogeny, which uses NNI to search for an optimal tree, at each step examines all neighbors of the current tree. I believe the whole tree is needed for likelihood computation. The neighborhood can be quite large for a few thousand units, so I added parallelization to it to save time.

Thanks, Teng

teng-gao avatar May 04 '22 16:05 teng-gao

Dear @teng-gao,
I only had a short look, but if it is about the the use of nni inside your numbat package, I am pretty sure the whole tree is not needed to compute the likelihood. Regards, Klaus

KlausVigo avatar May 05 '22 14:05 KlausVigo