Hi,

I've been trying to find out how (if) is it possible to analyse different partitions on the same tree (either through GUI or a batch file)... I mean, just one branch length estimation for each branch on the very same topology, so that I could get just ONE tree based on a partitioned data set... in case it's possible, could someone depict some code snippet showing the main steps for doing that?

Thanks in advance,

Jose_Patane.

Dear Jose,

Something like this ought to work.

[code]
DataSetFilter filter1 = (...);
DataSetFilter filter2 = (...);

define model, tree string here...

Tree T1 = treeString;
Tree T2 = treeString; /* same topologies */

ReplicateConstraint ("this1.?.?:=this2.?.?", T2, T1);
/* this will constrain all LOCAL (i.e. branch length
parameters in T2 to be the same as their counterparts
in T1, assuming the same model is applied to both trees.
If different models apply, additional steps are needed,
to scale parameters appropriately.
Look in messages.log to see what constraints have been
generated. */

LikelihoodFunction lf = (filter1, T1, filter2, T2);
Optimize (MLEs, lf);

etc...

[/code]

HTH,
Sergei

Thanks a lot, Sergei, I finally made it work!

Jose_Patane