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Our ability to correctly reconstruct the topology of a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes single-gene phylogenies particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilised in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. Because of their relevance to the understanding of the evolution of photoreception, a number of independent single-gene phylogenetic analyses have been performed to understand opsin evolution, but such studies inferred incongruent trees that hampered progress of our understanding of the evolutionary origins of animal vision. Here, we present a novel approach to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate the efficacy of our approach using two well-understood cases of long branch attraction in single gene datasets and simulations. After that, we apply our approach to a large collection of wellcharacterised opsins, and clarify early opsin evolution and the relationships of the three main opsin subfamilies.