Figure 1

Correlation-based networks of sequence-based methods. Seven major methodologies are summarized, including mutual information, machine learning (random forest, support vector machine, neural networks), Pearson coefficient, entropy theory, graphical models (Bayesian networks, singly connected spanning trees, mutagenetic trees), phylogenetic models and physicochemical property models. Methods are represented by cones (see abbreviations in Table 1) and the same color is given to sequence-based methods designed from similar methodologies (e.g. APC used MI as a part of its design, phylogenetic trees are used in Spidermonkey, CTMP and CoMap).