I want to build a evolutionary phylogenetic tree. for this i am following this article "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514880/".
According to this, I have selected single gene orthologus family and use muscle for each family alignment and build tree with Phylip JTT model. Finally, tree from each cluster was used for make a supertree using phylip consenses program. Now, I have single unrooted tree. I want to make the tree with evolutionary time."http://www.nature.com/nbt/journal/v31/n2/fig_tab/nbt.2478_F4.html".
Any kind of help would be highly appreciated.