Hi all
I am trying to use a partial (backbone) constraint in MrBayes, to force some relations that were postulated in another paper. As I understood from the command reference, I need to define a partial constrain with the monophyletic taxa in one side and the taxa I do not want to get in the middle of the other clade in the other:
constraint name partial = 41 42 48 : 14 15 16;
and them apply said constraint
prset topologypr=constraints(ingroup,name); [note I also have an ingroup constraint defined]
The analysis runs great, but in the end I got trees that do not fulfil the constraint at all.
Any ideas what is going wrong?
If you want to define a set of taxa as resulting in monophyletic you could use:
constraint NAME hard = taxon1 taxon2 ...;
prset topologypr = constraints (NAME);
As the command says it is a hard constraint, thus no other taxon can be placed within the monophyletic clade. If you would like to keep the possibility that yet non-included taxa could still be included, then replace the 'hard' by 'soft'.
Hope this helps,
Cheers, Patrick
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