Tree-building methods distance-based

Tree-building methods implemented in available software are discussed in detail in the literature (Saitou, 1996 Swofford et al., 1996 Li, 1997) and described on the Internet. This section briefly describes some of the most popular methods. Treebuilding methods can be sorted into distance-based vs. character-based methods. Much of the discussion in molecular phylogenetics dwells on the utility of distance-and character-based methods (e.g., Saitou, 1996 Li, 1997). Distance methods compute pairwise distances according to some measure and then discard the actual data, using only the fixed distances to derive trees. Character-based methods derive trees that optimize the distribution of the actual data patterns for each character. Pairwise distances are, therefore, not flxed, as they are determined by the tree topology. The... 

The paralinear or log-det transformation corrects for nonstationarity (see Swofford et al 1996). In this method, which is applicable only to distance tree building, the numbers of raw substitutions of each type and in each direction are tallied for each sequence pair in a fom-by-fom matrix as shown in Figure 14.7. Each matrix has an algebraic determinant, the log of which becomes a factor in estimating sequence divergence, hence the name log-det. Pairwise comparisons of sequences having various and assorted patterns of base frequencies will yield a variety of matrix patterns, giving a variety of determinant values. Thus, each estimated pairwise distance will be affected by the determinant particular to each pair, which effectively... 

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