How to reduce the number of constraints

[LuaBgd]

How to reduce the number of constraints

[josephwb]

@LuaBgd Are you certain there are no conflicting constraints? Even just 1 will make make an analysis impossible. For example, if there are any topological differences between your tree and the tree you referenced, then some constraints can be redundant or conflicting. I have (R) code that can check constraint consistency. If you post your tree & config file I can test things for you. If it proves useful I can clean it up a bit and put it in the treePL repo.

[LuaBgd]

Hi !

Thank you very much for your answer!
I am definitely not certain there are no conflicting constraints but I extracted them as follow:

• I extracted all node ages of a dated tree
• kept ages for nodes leading to a monophyletic group
• check in the phylogeny I want to date, if this node exists (is the same taxonomic group also monophyletic there?)
• removed contraints pointing the same node

So, I thought everything should be already consistent... But yes I can post the tree and the constraints, that would be lovely of you to look at it!

Thank you very much,
Luana

[Belinda333]

Hi everyone,

would it possible to share that R code to check constraint consistency? I have a similar issue and a lot of large trees to date where manually checking would take forever.... Thanks a lot!

Best wishes,
Belinda