Combine multiple species trees
Although I've never tried it myself, I think what you need can be achieved through the LogCombiner program from the BEAST package -- assuming the species trees files are comparable (ran with same parameters, same species names, etc.) I am also assuming that you meant 'five species tree files', each file with the posterior sample of species trees.

However, I do believe you should try to run all loci within the same analysis, or at least do some prior check to see if the distributions between data sets are comparable. LogCombiner assumes independent runs from the same data. 

I would also recommend taking a look (and following) the BEAST google group (which includes starBEAST discussions).