Most model-based molecular phylogenetic methods assume that the sequences diverged on a tree under homogeneous conditions. If evolution occurred under these conditions, then it is unlikely that the sequences would become compositionally heterogeneous. Conversely, if the sequences are compositionally heterogeneous, then it is unlikely that they have evolved under homogeneous conditions. We present methods to detect and analyse heterogeneous evolution in aligned sequence data and to examine—visually and numerically—its effect on phylogenetic estimates. The methods are implemented in three programs, allowing users to better examine under what conditions their phylogenetic data may have evolved.
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