Figure 2

Comparison of reconstruction methods. Comparison of distance functions and reconstruction methods. The graph shows how phylogenetic accuracy (c-score) is dependent on distance quality (δ value). Each distance matrix is associated with a certain δ value, which is lowest in case of best distance quality; each phylogenetic tree computed is associated with a certain c-score, which is highest in case of optimal agreement between the tree and the reference topology. For each distance matrix, trees were inferred using BIONJ (squares), FastME (circles), NJ (open inverted triangles), STC (diamonds), and UPGMA (triangles). To illustrate the behaviour of these individual methods of phylogenetic inference, cubic splines were used; the number of 15 degrees of freedom for the splines apparently optimal to summarize the shape of the data was found by careful optical comparison. For instance, the splines show that UPGMA performs relatively poorly with best distance values, whereas with high δ values (i.e., low distance quality) STC performs worst of all tree inference methods examined. See table 1 for a more detailed exploration of the interrelationships of topological accuracy, distance quality, and distance function parameters by multiple linear regression.