Abstract-Many applications in security, from understanding unfamiliar protocols to fuzz-testing and guarding against potential attacks, rely on analysing network protocols. In many situations we cannot rely on access to a specification or even an implementation of the protocol, and must instead rely on raw network data "sniffed" from the network. When this is the case, one of the key challenges is to discern from the raw data the underlying packet structures -a task that is commonly carried out by using alignment algorithms to identify commonalities (e.g. field delimiters) between packets. For this, most approaches have used variants of the Needleman Wunsch algorthm to perform byte-wise alignment. However, they can suffer when messages are heterogeneous, or in cases where protocol fields are separated by long variable fields. In this paper, we present an alternative alignment algorithm known as segment-based alignment. We show how this technique can produce accurate results on traces from several common protocols, and how the results tend to be more intuitive than those produced by state-of-the-art techniques.