I'm working with Agustus to predict genes. The question is what is the criteria to identify the closest related species among the list of already predicted genes. http://bioinf.uni-greifswald.de/augustus/ says "the human version is good for all mammals" since mammals are closely related species. Let me explain this with my scenario: I am trying to predict genes using Agustus on bacterium "Bradyrhizobium ganzhouense". There are 3 bacteria species already predicted according to the above site.
Which is the best species that can be used with Augustus from the above list to predict "Bradyrhizobium ganzhouense"? What is the criteria for choosing that? How can I identify the closest species among the above 3 to bacterium "Bradyrhizobium ganzhouense" which can be used with Augustus?
Any help appreciated and thanks in advance.