A simple and effective method for determining whether or not long branch attraction is affecting tree topology is the SAW method, named for Siddal and Whiting. If long branch attraction is suspected between a pair of taxa (A and B), simply remove taxon A ("saw" off the branch) and re-run the analysis. Then remove B and replace A, running the analysis again. If either of the taxa appears at a different branch point in the absence of the other, there is evidence of long branch attraction. Since long branches can't possibly attract one another when only one is in the analysis, consistent taxon placement between treatments would indicate long branch attraction is not a problem.