I have two orthologs from a populus tree species and want to know which will be the better ortholog ........can anyone tell me the way to determine that which ortholog will be better among the obtained two orthologs.
There always comes a result showing some score (bit score in case of blast based results), to decide which one is the best possible ortholog among the two. Try to find out the "score" or similar parameter to decide best from your results. As OrthoDB uses Smith Waterman algorithm along with CD-HIT you need to select the sequence getting maximum protein length coverage or amino acid sequence identity or both.
If still confused try to get function prediction by COG or GO or KEGG databases, the one has the similar function (if any) to your protein of interest (if at all its function is already known) that would be the best ortholog.