Hello Sergei I have a couple of questions for you...

1) First of all I am using the script dNdSRateAnalysis.bf and I wonder why whatever the codon model I use and whatever the  rate variation implementation (constant, nonsyn, dual etc) I get the tree window with the BL option of syn rates but no the nonsyn rates.

2) Indeed I try to do this by my self adding some code (from postdNdS.bf) at the bottom of the script. I get the nonsyn and the syn trees. But the syn tree is different to that of the tree window. This is maybe (??) because in the dNdSRate... script BL are estimated before the optimization of the likelihood function (??).
[code] /* is BL as will appear in window estimated here? */
initString = initString + "givenTree." + bn + ".synRate=nucTree." + bn+ ".t/codonFactor;";
                 }      
ExecuteCommands (initString);
[/code]


Hence if I put the added code (from postdNds.bf) before the optimization (just after the code above), then I get essentially the same syn rates of the object window. I indeed get a "nonsyn" rate tree  but non sure about what this really is.

Any help will be greatly acknowledged.

All the best,
Antonio

Dear Antonio,

You are not seeing the option for nonSynRates because of model parameterization (nonSynRates are functions of synRates). The easiest way to display syn and non-syn trees (scaled on the expected number of substitutions per codon) from the results of the analysis would be the following:

• Download the following batch file:  Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login
  
• Use File->Open Batch File to open the file from (1) in HyPhy
  
• When prompted for model fit, please choose the appropriate .fit file written out by the dNdSRates analysis.
  

You may also want to take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for some discussion of similar issues.

Cheers,
Sergei

Sergei, wonderful. Thanks a lot.   :D

All the best for you,
antonio