For this exercise we will use BEAST, which is probably the most used software for molecular clocks. It is freely available at http://beast.community/index.html.
BEAST uses bayesian methods for molecular phylogenies.
Alternatively, you can use the fast RelTime method implemented in the MEGA program. The detailed procedure is described here.
Some calibration points for molecular phylogenies can be obtained from the TimeTree database.
We will work based on this tutorial.