This invention relates to methods and devices for time transfer. The invention has particular application in the alignment of slave clocks to a master clock and dealing with packet delay variations. In embodiments of the invention, the slave clock uses the residence times measured by end-to-end transparent clocks to compensate for clock synchronization errors that arise due to variability in message transfer delays. Embodiments provide a simple linear approximation technique and a Kalman filter-based technique for estimating offset and skew of the slave clock.