AbstractMotivationThe structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many states, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range.ResultsWe here extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true node states. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from 5 different locations.AvailabilityThe here presented methods are combined into the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available athttps://github.com/nicfel/Mascot.git.