Parsimony searches

Distance matrix methods simply count the number of differences between two sequences. This number is referred to as the evolutionary distance, and its exact size depends on the evolutionary model used. The actual tree is then computed from the matrix of distance values by running a clustering algorithm that starts with the most similar sequences (i.e., those that have the shortest distance between them) or by trying to minimize the total branch length of the tree. The principle of maximum parsimony searches for a tree that requires the smallest number of changes to explain the differences observed among the taxa under study. 

As noted in the introduction, a major aim of the current research is the development of "black-box" automated reactors that can produce particles with desired physicochemical properties on demand and without any user intervention. In operation, an ideal reactor would behave in the manner of Figure 12. The user would first specify the required particle properties. The reactor would then evaluate multiple reaction conditions until it eventually identified an appropriate set of reaction conditions that yield particles with the specified properties, and it would then continue to produce particles with exactly these properties until instructed to stop. There are three essential parts to any automated system—(1) physical machinery to perform the process at hand, (2) online detectors for monitoring the output of the process, and (3) decision-making software that repeatedly updates the process parameters until a product with the desired properties is obtained. The effectiveness of the automation procedure is critically dependent on the performance of these three subsystems, each of which must satisfy a number of key criteria the machinery should provide precise reproducible control of the physical process and should carry out the individual process steps as rapidly as possible to enable fast screening the online detectors should provide real-time low-noise information about the end product and the decision-making software should search for the optimal conditions in a way that is both parsimonious in terms of experimental measurements (in order to ensure a fast time-to-solution) and tolerant of noise in the experimental system. 

The six aligned sequences in Fig. 1 were used to build amino add parsimony trees by PROTPARS in PAUP.13 An exhaustive search of the 105 alternative unrooted trees was performed the resulting distribution of possible trees was skewed14 positively, with a long tail (not shown) containing the shortest tree. This shortest unrooted tree (Fig. 2) requires 601 amino acid replacements the next shortest tree requires 625 events. In this case, the most parsimonious tree appears rather trustworthy. 

The combinatorial approach that was pursued in search of an antiasthma drug based on a split-and-mix strategy [92] as a practical use of the operational principle of parsimony was to get the most with the least in this case, to get 343 different types of variants in only 21 reaction steps. Scheme 1-17 sketches... 

Character-based parsimony methods search for the shortest length tree for the data as a best estimate of tree topology i.e. patterns of... 

The search for the shortest trees in tree space and the use of the cladistic version of the principle of parsimony, as implemented in computer programs... 

The cladistic parsimony principle, as understood by most users of computer programs, is utilized only in the search for the shortest tree. I have frequently heard cladists say that it should be impossible to discover an optimal tree topology by hand when many species are being considered, because there are millions of alternative topologies to be considered (e.g., about two million unrooted topologies for only 10 terminal taxa). As there exist more than 900,000 known species of insects and the number of alternative topologies that... 

Algorithms that implement a cladistic application of the principle of parsimony allowing the use of exact optimality criteria and (in principle) the exact search for the shortest trees... 

Morrone, J.J. and Carpenter, J.M., In search of a method for cladistic biogeography an empirical comparison of component analysis. Brooks parsimony analysis, and three-area statements, Cladistics, 10, 99-153, 1994(1995). 

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