Character-based phylogenetic

Phylogenetic analyses of sequences can be conducted by analyzing discrete characters (i.e., the nucleotides themselves) or by making pairwise comparisons of whole sequences (the distance approach). Deciding whether to use a distance-based or a character-based method depends on... 

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 third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

There are several important philosophical differences between distance-based phylogenetic methods and character-based parsimony which should not be overlooked. First is the unappealing property of distance-based analyses that all information on evolutionary change is averaged into one number for each pair of taxa. Second, to paraphrase Swofford and Olsen (1990), the as stamptions involved in distance methods (such as additivity and clock-like evolution) are rarely evident or discussed and the justification of the algorithm itself often seems to be the objective of the study. On the contrary, in the case of methods will a well-defined optimality criterion such as parsimony, the objective is usually related to a (more or less) concrete set of assumptions. 

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