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This work has focused on two atoms, Sr and Yb, due in part to the relatively high abundance of their odd isotopes, the use of which is necessary for appreciable direct excitation probability. The Sr clock transition has been measured (with an uncertainty of 20 kHz) using atoms in a magneto-optic trap (MOT), and has been excited with atoms confined in a one dimensional lattice. Here we report direct excitation of the Yb clock transition (at 578 nm) with atoms in a second-stage MOT, and the first fs-laser comb-based absolute measurements of the clock frequency for two different isotopes. These measurements lead to a nearly millionfold improvement in our knowledge of the transition frequencies, an important step toward Doppler-free spectroscopy of Yb atoms in a lattice.