Dr. Jahan,
Please refer to my reply to this old thread:
Basically, if you want to build a species tree, you can use tools available on the iTOL website to construct a newick format data file based on species you type in. Then other tools on the site can take that newick data and build a tree image from it. Unfortunately I am not an expert in this, so if you refer to that other thread (link above), thats the extent of my knowledge. But they have helpful documentation on iTOL. It is really a great resource.
John Martin