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.
For this, I would use simulation, see for example [Computational reconstruction of ancestral DNA sequences.][1]  
If you want experimental data, have a look at [An experimental phylogeny to benchmark ancestral sequence reconstruction][2].


  [1]: https://www.ncbi.nlm.nih.gov/pubmed/18629667
  [2]: https://www.nature.com/articles/ncomms12847