Full knowledge of the routing topology of the Internet is useful for a multitude of network management tasks. However, the full topology is often not known and is instead estimated using topology inference algorithms. Many of these algorithms use Traceroute to probe paths in the network and then use the collected information to infer the topology. In practice routers may severely disrupt the operation of Traceroute and cause it to only provide partial information. We propose iTop, an algorithm for inferring the network topology when only partial information is available. iTop constructs a virtual topology, which overestimates the number of network components, and then repeatedly merges links in this topology to resolve it towards the structure of the true network. We perform extensive simulations to compare iTop to state of the art inference algorithms. Results show that iTop significantly outperforms previous approaches and its inferred topologies are within 5% of the original networks for all the considered metrics.