A crucial building block for quantum information processing with trapped ions is a controlled-NOT quantum gate. In this Letter, two different sequences of laser pulses implementing such a gate operation are analyzed using quantum process tomography. Fidelities of up to 92.6(6)% are achieved for single-gate operations and up to 83.4(8)% for two concatenated gate operations. By process tomography we assess the performance of the gates for different experimental realizations and demonstrate the advantage of amplitude-shaped laser pulses over simple square pulses. We also investigate whether the performance of concatenated gates can be inferred from the analysis of the single gates.