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Over the past few decades, centralized computing systems have been replaced by decentralized systems, consisting of simple nodes interconnected by a communication network. The time reference of the distributed nodes must be synchronized in order to be able to coordinate the operation or compare the data collected by the different nodes. Several synchronization protocols have been developed to be used instead of global positioning system or dedicated synchronization systems. For example, the network time protocol (NTP) is a very popular synchronization protocol used to synchronize computers over wide area networks, like the Internet. In addition, IEEE 1588, a synchronization protocol dedicated to high-performance synchronization in local networks, was recently established. However, submicroseconds synchronization can be obtained only using dedicated hardware devices, thereby increasing the cost of each node. For these reasons, PTP software-only implementations are quite common in real systems, with a resulting synchronization uncertainty varying from a few to hundreds of microseconds and quite burdensome to estimate or measure. The work presented in this paper focuses on the analysis of the major uncertainty contributions in a software-only implementation. Particularly, a careful analysis of timestamp mechanism and time management in a PC platform is carried out. In addition, a method for the experimental evaluation of uncertainty contributions is proposed. A test case based on a software implementation of the IEEE 1588 (the so-called PTPd) is presented. The experimental tests presented in the paper highlight that the main uncertainty source of a software-only synchronization approach is the timestamp method. Timestamping accuracy can be affected by the computational load of the node itself: in normal conditions, the maximum uncertainty introduced by the timestamp mechanism is in the order of 10 , but in case of high computational load, it can raise up to 224 - C;s.