Hi,

I'd like to implement a Relative Ratio Test using the RelativeRatio.bf but I want to leave one branch free.
Is it possible to do that?

Thanks,
L.

Dear Luli,

Yes; but you need to modify the source code of RelativeRatio.bf. Paste this code:

Code (]
mxTreeSpec = {5,1};
mxTreeSpec [0):

= "tr2c"; mxTreeSpec [1] = "8240"; mxTreeSpec [2] = "10,40,-10,-175,1"; mxTreeSpec [3] = ""; mxTreeSpec [4] = ""; OpenWindow (TREEWINDOW, mxTreeSpec);                                           internalNodes = BranchCount(tr2c); leafNodes        = TipCount (tr2c); choiceMatrix = {leafNodes+internalNodes,2}; for (bc=0; bc<leafNodes; bc=bc+1) {      choiceMatrix[bc][0] = TipName(tr2c,bc);      choiceMatrix[bc][1] = "Taxon " + choiceMatrix[bc][0]; } for (bc=0; bc<internalNodes; bc=bc+1) {      choiceMatrix[bc+leafNodes][0] = BranchName(tr2c,bc);      choiceMatrix[bc+leafNodes][1] = "Internal Branch Rooting " + tr2c[bc]; } ChoiceList  (stOption,"Do not constrain:",0,NO_SKIP,choiceMatrix); if (stOption[0] >= 0) {      for (k=0; k<Columns (stOption) * Rows (stOption); k=k+1)      {            ExecuteCommands ("ClearConstraints (tr2c."+choiceMatrix[(stOption[k])][0]+");");      } }

into the RelativeRatio.bf file immediately after  
[code]
ReplicateConstraint (constraintString,tr2c,tr1c);
[/code]

The code will prompt you to select one or more branches which you do not wish to constrain with the Relative Ratio test.

Cheers,
Sergei

Hi Sergei,

Thanks a lot for your promptly  response!

I modified the bf file adding the piece of code that you sent me.
Everything was going perfect until I received the following message:
[...] must be preceded by a matrix variable: "ClearConstraints(trc."+choice Matrix[(s+Option[k])][?0]+");"
Current BL Command: ExecuteCommands in string("ClearConstraints (tr2c."+choiceMatrix[(stOption[k])][0]+");");

Could you help me with this error message?
Thanks a lot,
L.

Dear Luli,

This error occurs because I used a coding shortcut not understood by HyPhy versions which are over 3 months old. It will go away if you download a newer (April 2006 or later) version.

Cheers,
Sergei