Parsimony methods results

The home page of WebPhylip consists of three windows. The left window is the command window for selecting and issuing the execution (Run) of the analysis/ operation. The analysis results appear in the upper window. The lower window is the query window with options, a query box for pasting the query sequences (in Phylip format), and Submit/Clear buttons. To perform phylogenetic analysis, select DNA/Protein for Phylogeny method in the left window to open the available analytical methods (parsimony, parsimony + branch bound, compatibility, maximum likelihood, and maximum likelihood with molecular clock for DNA whereas only parsimony for protein). Click Run (under the desired method) to open the query window with options. Select the appropriate Input type (either interleaved or sequential), paste the query sequences and click the Submit button. The analytical results are displayed in the upper window (Figure 13.4). 

So what does one need to do First, the three methods obviously may not provide the researcher with the same resultant model. To pick the best model requires experience in the field of study. In this case, using the backward elimination method, in which all x, variables begin in the model and those less significant than F-to-Leave are removed, the media concentration was rejected. In some respects, the model was attractive in that and s were more favorable. Yet, a smaller, more parsimonious model usually is more useful across studies than a larger, more complex one. The fact that the interaction term was left in the model when X2 was rejected makes the interaction of Xj x X2 a moot point. Hence, the model to select seems to be the one detected by both stepwise and forward selection, y = ho + 2 2, as presented in Table 10.5. 

Bootstrapping is a resampling tree evaluation method that works with distance, parsimony, likelihood, and just about any other tree derivation method. It was invented in 1979 (Efron, 1979) and introduced as a tree evaluation method in phylogenetic analysis by Felsenstein (1985). The result of bootstrap analysis is typically a number associated with a particular branch in the phylogenetic tree that gives the proportion of bootstrap replicates that supports the monophyly of the clade. 

This is well documented by the appeal to total evidence (Kluge, 1989), which is a methodological requirement invoked for cases in which inductive reasoning yields contradictory (or inconsistent) results (e.g., Hempel, 1965 63-64). The necessity for an appeal to total evidence highlights the inconsistent (i.e., contradictory) distribution of characters across taxa, whereby parsimony is a method that sorts out characters and terminals in terms of a logically subordinated hierarchy in a pattern that maximizes support for inclusion but minimizes conflict. By allowing conflict, parsimony analysis accounts for the messiness of... 

There are still numerous discussions about the best methods in phylogenetic studies. Our previous studies, however, demonstrate the strong congruence in results of analyses of the same datasets by methods of direct optimization and parsimony (Huttunen and Ignatov, 2004) and by methods of direct optimization, parsimony and maximum likelihood (Gardiner et al., 2005). We believe that this congruence can serve as additional support for the results obtained. 

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