PhyML run with constrained tree

[fxjonas]

Dear Stephane,

I am trying to use the --constrain_file option to constrain the topology of the tree.
However, I run into several problems:
A) it seems to me that the cosntraining tree has to be of a certain structure, i.e. branches with more than two nodes are only allowed at the highest layer of the tree:
while
((A,B),C,(D,E,F)); the example in the manual) gives segmentation error / tree structure error.
((A,B),C,D,(,E,F)); does not.

are you using this option? is it supposed to work with trees like the first one? It would be really useful to be able to handle this constrains, but maybe I am doing something wrong so it would be great if you could give some more detail on how to build the trees for this option.

B) When trying to combine the --constrain_file option with mpi-run it somehow doesn't work (segmentation error) and it also crashes sometimes during the bootstrapping. Is it possible that this option makes phyml less stable?

Thanks for your help.
Felix

[stephaneguindon]

Dear Felix,
The two constraint trees you give seem fine to me. PhyML should be able to use either of them. It could be the case, however, that the input tree you gave in your analysis does not fulfill the constraint, in which case PhyML has no way to move forward in the optimization. Would you mind sending me the data set you used here along with the corresponding command line?
As for combining the bootstrap with constraints, I would need to review that part of the code to make things more stable. I will keep you updated.