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Search Results: Parallel computer processing in systematics

A central goal of evolutionary biology is the reconstruction of the tree of life. All life, both living and extinct forms, is thought to have...


= Encyclopedia Article; = Research Update
Figure 1.Alternative alignments for four sequences on a tree. The sequences (GGGG, GGG, GAAG, GAA) are aligned with two evolutionary trees. (a) The simplest arrangement for the top alignment is the top evolutionary tree (costing six evolutionary steps, denoted by lines and arrows, because in both scenarios insertion and deletion of nucleotides is weighted as two nucleotide substitutions) and (b) that for the bottom alignment the bottom tree (also costing six evolutionary steps). Mismatching the alignments and trees (top alignment with bottom tree, and vice versa) results in scenarios that cost an additional evolutionary step.
Figure 2.Graphs illustrating the parallel efficiency of the core algorithms of POY in a large PC/LINUX computing cluster in service at the American Museum of Natural History. The solid plots indicate the best speedup of tree-based alignment (measured in trees examined per second) that can be expected as a function of the addition of processors. The dashed plots indicate the actual speedup during testing. (a) Parallel building (using many processors per tree) is inefficient, whereas (b) multibuilding (using one processor per tree) is very efficient.
Figure 3.Example of fault tolerance in cluster computing. (a) A cluster that is logically structured, in which one master node and six slave nodes have to solve a problem that can be divided into 30 subproblems that can each be solved on a slave node. When the first 17 subproblems have been solved, the slave node that deals with subproblem 19 becomes unavailable because of a failure in that node or in the connection of that node to the cluster. (b) The master node reacts to this by removing that node from the resources that it will use and by rescheduling subproblem 19.
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