From the MrBayes tree output files, which trees tree.con file can be used? The tree1.con or tree2.con?

Question

[willianarcunha]

Hello, I am using MrBayes 3.2.6. A bayesian inference generates two tree files (tree1.con and tree2.con) which one is my tree? What criteria do I use to decide?

Thank you!

Answer 1

[Brett]

This is a few years late, but I had the same problem and after several hours of troubleshooting, figured it out. I had used PartitionFinder2 to find the best partitions and substitution models for my multi-locus dataset. I copy-pasted the output bayes block to my nexus file to be read by MrBayes3.2.7. Turns out, there was a command in this block that was causing the error: "unlink brlens=(all)". After removing this command and running a test run, I am now only getting 1 consensus tree after the sumt command. Hope this helps someone.