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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> Correcting for Numerical Underflow http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1234881901 Message started by Miguel Lacerda on Feb 17^th, 2009 at 6:45am

Title: Correcting for Numerical Underflow
Post by Miguel Lacerda on Feb 17^th, 2009 at 6:45am

Dear Sergei,

I am trying to compute site likelihoods for a given model using LFCompute and am getting log-likelihoods of -1e06 for many of the sites. Is there a way to correct for numerical underflow in HyPhy?

Thanks,
Miguel

Title: Re: Correcting for Numerical Underflow
Post by Sergei on Feb 17^th, 2009 at 8:09am

Dear Miguel,

Does this happen in the new build as well?
The version from SVN should have a pretty robust underflow correction algorithm.

Cheers,
Sergei

Title: Re: Correcting for Numerical Underflow
Post by Miguel Lacerda on Feb 17^th, 2009 at 8:36am

Sergei,

I am using the SVN build version 298 - is that the version you are referring to?

Miguel

Title: Re: Correcting for Numerical Underflow
Post by Sergei on Feb 17^th, 2009 at 9:23am

Hey Miguel,

I think the build version is up to 410 or something like that now.
At any rate, 298 should have dealt with the underflow. Can you send me an example (data/bf) where the overflow happens?

Cheers,
Sergei