. 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.