Tree-building

Turba (fol. 89) Take the white tree build about it a round and gloomy house surround it with a tower and put therein a centenarian. Then shut it up so that no wind or dust can get to him. Leave him there eight days. I say to you that the same man must not cease to eat of the fruit of the tree until he grows young again. 0 what a wonderful quality Here is the father become a son, and bom again. 

Maximal-Tree Building. To build the maximal tree, one needs to choose the best splitter to divide each root node into two child nodes. The measure of a good split is the impurity decrease between the parent node and its children ... 

Phylogenetic tree building seems to be more difficult for plants than for animals, and varying results have been reported even using the ancestral sequence approach 123,124). For the moment these trees must be considered only tentative. 

Terrain, including the presence of vegetation/trees, buildings, and other stractures... 

Character-state weight matrices have usually been estimated more or less by eye, but they can also be derived from a rate matrix. For example, if it is presumed that each of the two transitions occurs at double the frequency of each transversion, a weight matrix can simply specify, for example, that the cost of A-G is 1 and the cost of A-T is 2 (Fig. 14.5). (The parsimony method dictates that the diagonal elements of the matrix, or the cost of having the same base in different sequences, be zero. This proves to be a shortcoming of parsimony this will be discussed further below.) In the subsequent tree-building step, this set of assumptions will minimize the overall number of transversions and tend to cluster sequences differing mainly by transitions. 

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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