Hello,
I have some trouble when trying to import BayesTraits results on TreeGraph2. I have tried several options but the software keep telling me " "the following MRCA/node definitions could not be reconstructed because one or more of the referenced terminal nodes is not contained in the current tree document".
Initially, my nexus tree did not have any internal node name. The latter were created by TG2, which I used to generate BayesTraitsInput. I have tried with "InteralNode1" format or IDs like "3f3d9jwj7s", with or with < ' >. Still impossible to reimport the log file...
Do you have any clue how I could solve this issue ?
Thank you
Hi,
the internal node names (or the unique node names, TreeGraph 2 assigns to each node in addition) are not relevant for importing BayesTraits data. As the error message states, one or more TERMINAL nodes have not been found. At the beginning of each BayesTraits log file, a set of reconstructed internal nodes is defined by enumerating the terminal nodes nested under each of them. (Actually, this definition would even allow to to reference different internal nodes in different topologies, e.g., in a Bayesian context, but this is only additional information.)
When TreeGraph reads such a file, it searches for internal nodes that nest all the terminal nodes that have been defined by BayesTraits. If the tree does not contain one or more of these, it will give this error message. Either some terminal nodes are missing in your tree, or their names differ (e.g., some have additional trailing whitespaces or underscored in one file and spaces in the other). You can adjust how names should be compared.
Another reason could be that you selected the wrong node/branch data column as the reference. If the names are, e.g., contained in the "node names" column and you selected to look for them in another columns, mapping also will not work.
TreeGraph should have given you a list of terminal nodes, it did not find. Did you check, if these were in the tree or not?
If this does not solve your problem, feel free to contact me again. Also note that currently only the output of BayesTraits 2 is supported and not of the recent version 3, which changed its output format.
More information is also available in the documentation: http://treegraph.bioinfweb.info/Help/wiki/Importing_ancestral_state_probabilities_from_BayesTraits
Best
Ben
Thank you a lot for your answer ! Indeed, the problem seems to be the "_" between genus and species name. With shorter names, I could import my data !
Best,
Benjamin
Glad that we could solve that.
Note that there is also an option to "Distinguish between space (" ") and underscore ("_")" that may solve such problems. This is available for both importing BayesTraits data and for importing annotations from tables.
- http://treegraph.bioinfweb.info/Help/wiki/Importing_ancestral_state_probabilities_from_BayesTraits#Leaf_names
- http://treegraph.bioinfweb.info/Help/wiki/Importing_node/branch_data#Compare_options
- Badges
- Science topic
- Similar topics
- Filing