Dears,

    i have certain questions on parris usage in hyphy as well as datamonkey...i kindly request you to answer them

1. Would you recommend or discourage using parris as preliminary test for   
    selecting candidate genes for further site wise selection analysis?

2. Is there is way to know whether parris has detected and used any   
    recombination breakpoint in its analysis?

3. I get different phylogenetic tree topology when same alligned CDS data is   
    analysed on datamonkey and on local hyphy(maximum likelihood   
    method>MG94>global>total branch length),both using NJ method? Though this is   
    said to have very little effect on results, i would like to know the reason   
    for this difference(does datamonkey use star phylogeny)? 

4. While running parris on datamonkey the selected nucleotide model changes in   
    the final step e.g. 012230 becomes 012240,010020 becomes 010040..why does this   
    happen? 

5. For parris result carried on datamonkey.. i consistently get p value of 1   
    and hence accepting the null hypothesis..LRT close to 0, both models having   
    almost same likelihood value..my 13 sequence alignments seem to be proper..   
    why does this happen?
 
6. What is the setting for parris on hyphy to be same as one on datamonkey?ei   
    rate variation model = constant/proportional/dual/non-syn? 
    it uses codon model or nucleotide model for branch length estimation?
    whether the distribution is 'parris'? 

7. Would you enligthen me a bit on analysing parris results in hyphy?

8. Whether GA branch method is applicable for mammalian sequences to detect   
    When did the selection occur(temporal model)? Does it make assumption of uniform 
    background as in hyphy  TestBranchDNDS.bf?
    
    Does CompartmentalizationSelectionLRT.bf makes the same assumption of uniform   
    background with respect to selected clade?

9. Whether spatial rate variation obtained from SlidingWindowAnalysis.bf can be   
    extrapolated for protein structure analysis with respect to positive selected   
    regions in polypeptide chain?

    thanking you,
    regards,
    sunil

Dear Sunil,

Your questions have just been pointed out to me - I'll try to answer the ones relating to PARRIS below.

Hope this helps,
Konrad Scheffler

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Yes, that is the idea. PARRIS (the downloadable version for HyPhy) also does sitewise selection analysis, although the DataMonkey version does not.

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PARRIS does not scan for recombination - you need to feed it the recombination breakpoints as detected using a breakpoint detection program. Currently, the easiest way to do this is to use GARD and send its output to PARRIS. This is easy to do on DataMonkey, and the HyPhy version also accepts GARD output.

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I don't know - hopefully Sergei can answer this. I would be wary of incorrect topologies, after all recombination effectively causes false positives by messing up the topology.

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Could be a bug - Sergei?

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This means that the alignment does not contain significant evidence for positive selection. I.e. after taking account of recombination breakpoints (if specified) and the fact that synonymous rates may vary (which can also be an artefact of recombination), there is no need to assume presence of positive selection in order to explain the data. This does not mean that positive selection is necessarily absent, but it does mean that you do not have enough evidence to infer its presence.

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dual

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I assume Sergei implemented it to use the nucleotide model.

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I assume you are asking where in the distribution PARRIS is: it's in the folder Contributions/Possel_in_recomb/

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You need to be more specific with your question. PARRIS writes many results; hopefully some/most of them are self-explanatory.
 
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The HyPhy script also does the LRT automatically - p-values are reported in the result files. If you prefer you can use the AIC instead - both methodologies should be valid in this case.

Dear Sunil,


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Different distance metric => different tree.
Datamonkey uses TN93, which is nucleotide based.

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012230 is equivalent to 012240, so are the other two. I believe this has already been addressed in an earlier post: Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login



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Correct assumption.

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It is under the Selection/Recombination rubrik in Standard Analyses; I moved it from Contributions about 6 months ago.

Cheers,
Sergei