Is there gold standard data for ancestral reconstruction? I am asking because I am trying to create a new approach for ancestral (gene/protein sequence) reconstruction (using a algorithm that has not been used before for this) and I wanted to compare the performance of current tools like MrBayes, MEGA, Mesquite etc.
Is there a way to compare their performances based on some gold standard data? I would like to use the same data to check the efficiency of my new approach.
It's hard for me to believe that there wouldn't be any such dataset, given that so many tools provide this service.
Any help would be appreciated.
did you check the papers describing those tools? perhaps they mention some sort of dataset?
In the papers for these tools, they do not report any dataset, just the fact that they provide these services. The papers of MrBayes has only the mathematical model used, the papers for MEGA provide performances but not for ancestral reconstruction, and I was unable to find the corresponding paper for Mesquite