Hi Sergei,

I am just trying to reroot many trees using a batch file, those trees come from a previous NJ. Then I want to use those trees for an analysis with the PAML package.

I find a strange problem, the output rerooted trees of the batch file cannot be readed by PAML, however if I do the same in the GUI of Hyphy, the output rerooted trees can be readed by PAML. For example:
Tree from GUI:
(outgroup:0.10175,((((seq00002:0.00712982,seq00005:0.00294759):0.000123234,seq00
007:0.00289186):0.0118193,(seq00003:1e-05,seq00010:1e-05):0.0210865):0.00905762,
((seq00001:0.00278719,(seq00004:0.00598958,seq00008:0.00815702):0.000217613):0.0
0276009,(seq00006:0.00100167,seq00009:1e-05):0.0103881):0.0227801));
Tree from Batch file:
((((((seq00002:0.00712982,seq00005:0.00294759):0.000123234,seq00007:0.00289186):
0.0118193,(seq00003:1e-05,seq00010:1e-05):0.0210865):0.00905762):0.00905762,((se
q00001:0.00278719,(seq00004:0.00598958,seq00008:0.00815702):0.000217613):0.00276
009,(seq00006:0.00100167,seq00009:1e-05):0.0103881):0.0227801):0.10175,outgroup:
0.10175);

I think both of trees are good, the only one difference is the position of the outgroup. However PAML only likes the first of them, for the other writes:
Error: check #seqs and tree: perhaps too many '('?.

So, maybe it is a bag of PAML. But well, I think perhaps there is a way for obtaining the first rooted tree using a batch file of Hyphy because with the GUI that is possible, is there any way?.

Below, I send you the part of my batch file about this:
[code]/* define the model JC */
     equalFreqs = {{.25}{.25}{.25}{.25}};
     JC69 = {{*,a,a,a}{a,*,a,a}{a,a,*,a}{a,a,a,*}};
     Model JC69model = (JC69, equalFreqs);
     UseModel (JC69model);

     /* build NJ */
     distanceChoice = 0; /* raw distances */
     modelType = 0; /* no rate variation*/
     methodIndex = 1; /* Negative Branch Lengths are Allowed */
     p = InferTreeTopology(1.0); /* in myFunctions.bf */
     treeString = TreeMatrix2TreeString (1); /* treeString stores the tree in Newick format */
     treeString = RerootTree (treeString,0);
     fprintf (stdout,"\nInferred NJ tree: ", treeString);

     OutFile = inputfile + "_tree.tre";
     fprintf (OutFile,CLEAR_FILE);

     fprintf (stdout, "\t[WRITING tree TO ",OutFile,"]\n");            
     fprintf (stdout, "\n\nTree NO Rooted:");      
     fprintf (stdout,"\n", treeString);
     
     NICETY_LEVEL = 3;

     fprintf (stdout, "\n\nOther trees:");      

     Tree treeRoot_outg = treeString;
     fprintf (stdout,"\nInferred NJ tree (before rooting with outgroup, without branch lengths): ", treeRoot_outg);
     fprintf (stdout,"\n");

     treeRoot = RerootTree(treeRoot_outg,"outgroup");
     fprintf (stdout,"\nInferred NJ tree (after rooting with outgroup): ", treeRoot);
     fprintf (stdout,"\n");
     [/code]


Thanks a lot.   :D
Regards,

Miguel

Dear Sergei,

Hyphy is the best, I know, D. Posada (my boss) tell me that always  . Hyphy is the most flexible to use, it is perfect for complete analysis where you can study many different things in only one step. That is great!!   

Well, I was using PAML (baseml) for an analysis of "marginal" reconstruction of ancestral sequences.

Looking to your answer, this is something apart of this, let me tell you about I also need to do an analysis of positive selection sites (no branches, only the question: what sites have positive selection?). Also I saw PAML could do this by codeml, but I think Hyphy is the best specially for this analysis.
Hyphy has many batch files for this:
NielsenYang.bf
CompareSelectivePressure.bf
MFPositiveSelecton.bf
QuickSelectionDetection.bf
- What is the best of these batchs for this analysis?, I think NielsenYang.bf, but what is your opinion?
- Maybe, is there any batch file for this analysis without the prompt questions?, for do a GY94 1x4, cutoff 0.9 and 8 categories. The idea is to analyze many data sets. If it is not, there is not problem, I am going to work on that very soon.

Finally, let me come back to the rerooting trees question. I think it could be two options to obtanin the tree1 (trees of the previous topic) in the batch file:
First, Is there any way in Hyphy for changing the position of the "outgroup" sequence in the batch file (convert the tree2 in the tree1)? or Second, use a different way to reroot the tree in the batch file for obtaining the tree1, like the GUI works.

Regards, 
Miguel

Dear Sergei,

Great, so Ok I would like to try the marginal reconstruction of the new version. Let me know when you finish it.      

Thanks for your recommendation about estimate positive selection by site. I am going to see those options.      

About the question of rerooting trees    , I mean if you look at the two trees that I send you in the first message, both of trees come from the same data file, and each tree comes from a different "way or methodology" in hyphy (the first comes from the GUI and the second comes from my batch file which I also attached in the first message), you can see that both of them are the same tree but the newick format was wrote in a different way. Right?
Then, other programs (like PAML or FigTree, FigTree said "Missing ',' in tree") do not read the newick tree from my batch file (but they read the newick tree from GUI), very strange but I think that it is a problem of the other programs.  
I have to work with many data sets so I will need to use a batch file of hyphy. So I asked you if it was possible to obtain from the batch file the rooted tree in the same newick than the rooted tree from the GUI.
Well, that is very difficult to explain    , it does not matter, I will find another way to obtain many NJ rooted trees that the other programs can read.


Again, thanks a lot for all and for your answer so fast,    
Regards,

Miguel

Dear Sergei,

Ok, I will be waiting for your code to change the position of the outgroup (please let me know if that is not possible) and for the new batch file on marginal ancestral sequence reconstruction.

Take care, 

Miguel

Dear Miguel,

You can recover the ancestral sequences under any evolutionary model in HyPhy. To reconstruct amino-acid sequences, you need to either fit a codon (assuming you have codon inputs) or an amino-acid model to the data.

Cheers,
Sergei

I get it!!.  


Regards,

Miguel