Among the criteria to evaluate the performance of a phylogenetic method, 
robustness to model violation is of particular practical importance as complete 
a priori knowledge of evolutionary processes is typically unavailable. For 
studies of robustness in phylogenetic inference, a utility to add well-defined 
model violations to the simulated data would be helpful. We therefore introduce 
ImOSM, a tool to imbed intermittent evolution as model violation into an 
alignment. Intermittent evolution refers to extra substitutions occurring 
randomly on branches of a tree, thus changing alignment site patterns. This 
means that the extra substitutions are placed on the tree after the typical 
process of sequence evolution is completed. We then study the robustness of 
widely used phylogenetic methods: maximum likelihood (ML), maximum parsimony 
(MP), and a distance-based method (BIONJ) to various scenarios of model 
violation. Violation of rates across sites (RaS) heterogeneity and simultaneous 
violation of RaS and the transition/transversion ratio on two nonadjacent 
external branches hinder all the methods recovery of the true topology for a 
four-taxon tree. For an eight-taxon balanced tree, the violations cause each of 
the three methods to infer a different topology. Both ML and MP fail, whereas 
BIONJ, which calculates the distances based on the ML estimated parameters, 
reconstructs the true tree. Finally, we report that a test of model homogeneity 
and goodness of fit tests have enough power to detect such model violations. The 
outcome of the tests can help to actually gain confidence in the inferred trees. 
Therefore, we recommend using these tests in practical phylogenetic analyses.