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Return branches with sites with FUBAR (Read 2046 times)
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Curious HyPhy user

Posts: 1
Return branches with sites with FUBAR
Oct 17th, 2013 at 8:16am
I'm trying to use FUBAR in place of the branch-site REL method in order to enjoy the computational speed-up; however, I do not see a straightforward way to return the branches and sites under selection in the output. I would like to estimate the proportion of sites under positive selection for each branch for 12,000 gene clusters. I'm able to run FUBAR just fine on our cluster non-interactively, it's just a matter of returning for each branch for each site if that site is under selection in the csv output file. Is it feasible for FUBAR to return this lineage-specific information?
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Datamonkeys are forever...

Posts: 1658
Gender: male
Re: Return branches with sites with FUBAR
Reply #1 - Oct 31st, 2013 at 3:18pm
Hi Jorge,

Unfortunately, there is no way of extracting branch-specific information from FUBAR, as the model explicitly assumes that omega is constant from branch to branch. We have some methods in the works for doing a FUBAR-style branch-site REL model, but those haven't been finished yet

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