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Phylogenetic methods from evolutionary biology have been used in recent years for stemmatic analysis of manuscript and other traditions. However, some scholars have criticized the applicability of these methods. We review the methods used and the criticisms made. We argue that many of the criticisms arise from a misunderstanding of present methods. While other criticisms may be valid, they also apply to conventional stemmatic analysis. We argue that a combination of phylogenetic methodology and traditional scholarship is likely to be the most useful.