Your post is lacking details. You have 987 proteins, or 987 contigs? Protein or DNA tree? What does 10 numbers mean: 10 related species, or you want to do 10 trees? It is difficult for me to expend major effort, and I suspect for others as well, when you are willing to write only 2 sentences about your problem.
I would not normally do this using a pre-packaged pipeline as there are many things to be customized. However, since you seem to be new to this topic, here goes:
It boils down to finding shared single-copy markers present in all species, aligning them individually, concatenating into a super-matrix, and building trees. A simpler but less accurate approach is to pick a couple of individual proteins (or rRNA) to build trees. I suggest you research this well before doing anything, as it is decidedly non-trivial.