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HYPHY Package >> HyPhy feedback >> GARD results interpretation http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1177651272 Message started by olorin on Apr 26th, 2007 at 10:21pm |
Title: Re: GARD results interpretation Post by Sergei on Apr 27th, 2007 at 10:34am
Dear olorin,
wrote on Apr 26th, 2007 at 10:21pm:
It is indeed a conservative check, but then again one always has to balance between power and accuracy. Quote:
Not likely, unless they used a poor model (e.g. disallowing site-to-site rate variation). You can actually check for this using the GARD postprocessor file - it fits the same tree to all putatively recombinant fragments, but allows branch lengths to vary - this gives you a null model of rate variation to test against as well. Quote:
In the GARD paper we did a number of simulations to that effect - the breakpoints are usually quite accurate without any additional verification (but one should use model averaged breakpoint locations to incorporate the noise). One can easily eliminate rate variation by using a sufficiently general model. Cheers, Sergei |
Title: Re: GARD results interpretation Post by olorin on May 1st, 2007 at 8:49pm
Dear Sergei,
Thanks. Your reply is most helpful. I will put further thoughts in this matter. olorin |
Title: Re: GARD results interpretation Post by gregonomic on May 16th, 2007 at 8:54am
I'm a bit confused. In your Mol Biol Evol, 2006, 23(10):1891-1901 paper, under the 'Biological Data Analyses' section, you say:
Quote:
Please clarify. |
Title: Re: GARD results interpretation Post by Sergei on May 16th, 2007 at 9:34am
Dear Gregonomic,
Traditional rate variation along the sequence (i.e. the kind that affects all branches in the tree) can be easily modeled with existing models (e.g. gamma rate variation); one can however imagine a more involved process where only parts of the tree are affected by rate/model variation (e.g. heterotachy) - if enough branches are involved, or if the variation shortens some branches and lengthens others at a given site, then the method can be confused. HTH, Sergei |
Title: Re: GARD results interpretation Post by gregonomic on May 17th, 2007 at 2:21am
Thanks Sergei.
So, technically, they weren't wrong when they said the supposed recombination might have been an artifact of "substitution rate variation", they just weren't as specific as they could/should have been? They don't say anything about the number or length of putative recombination fragments, so it's hard to know whether olorin's suggestion (ie. that there isn't enough phylogenetic signal for the SH test to pick up the recombination) is correct. A related question: does the GARD post-processor run a KH or SH test? Is the SH test considered more rigorous? Greg. |
Title: Re: GARD results interpretation Post by Sergei on May 17th, 2007 at 8:14am
Dear Greg,
You are quite right in saying that there exist substitution rate variation scenarios which may confuse any recombination detection method: e.g. convergent evolution along a sequence region can be considered one of them (i.e. changes in substitution rates which modify the nature, not just the speed, of the substitution process). That said, in recombination detection literature, 'rate variation' is usually assumed to be the typical site-to-site rate variation (e.g. in the Posada/Crandall PNAS simulation paper). I should have been more specific in the GARD paper discussion and qualified substitution rate variation :) SH and KH tests are identical when only two fixed trees are involved - sorry for loose terminology on my part. Going back to the JVI paper; it's indeed difficult to verify the claims not having the data at hand; however, really short or low sequence divergence fragments that do not support any phylogeny particularly well (i.e. have similar likelihood scores on a number of phylogenies) also will not likely be the primary contributors to the c-AIC improvement, i.e. if there had been any strong c-AIC derived signal, it would have likely come from fragments that support a particular type of phylogeny. Cheers, Sergei |
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