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. Author manuscript; available in PMC: 2008 Mar 20.
Published in final edited form as: J Proteome Res. 2006 Sep;5(9):2236–2240. doi: 10.1021/pr0504485

Table 1.

The Advantages of Phylogenetic Analysis over Statistical Cluster Analysis

phylogenetic analysis cluster analysis
■ produces a classification based on shared derived similarities and reflects phyletic relationships ■ produces a classification based on overall similarity and may not reflect phyletic relationship
■ uses one algorithm for the analysis of all types of cancers ■ may require a specific algorithm for each cancer type
■ discriminates between ancestral and derived states; uses only derived character states (apomorphies) ■ does not discriminate between ancestral and derived character states; uses both
■ resolves issues of parallelism (multiple independent origins) by parsimony or maximum likelihood ■ does not resolve issues of parallelism
■ offers predictivity ■ does not offer predictivity.