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A phylogenetic tree is used to present the evolutionary relationships among the interesting biological species based on the similarities in their genetic sequences. The UPGMA is one of the popular algorithms to construct a phylogenetic tree according to the distance matrix created by the pairwise distances among taxa. To solve the performance issue of the UPGMA, the implementation of the UPGMA method...
In order to infer evolutionary relationships as well as reconstruct phylogenetic trees, evolutionists often employ two general approaches: character-based and distance-based. Inasmuch as character based methods could be inordinately expensive in computational process, researchers have to use some estimation methods with practical run time. In this context, distance based methods are exceedingly quicker...
Phylogenetic analysis is commonly used to analyze genetic sequence data from fungal communities, while ordination and clustering techniques commonly are used to analyze sequence data from bacterial communities. However, few studies have attempted to link these two independent approaches. In this paper, we propose a method, which we call spherical phylogram (SP), to display the phylogenetic tree within...
The construction of phylogenetic trees is important for the computational biology, especially for the development of biological taxonomies. UPGMA is one of the most popular heuristic algorithms for constructing ultrametric trees (UT). Although the UT constructed by the UPGMA often is not a true tree unless the molecular clock assumption holds, the UT is still useful for the clocklike data. However,...
The order of genes in genomes provides extensive information. In comparative genomics, differences or similarities of gene orders are determined to predict functional relations of genes or phylogenetic relations of genomes. For this purpose, various combinatorial models can be used to identify gene clusters-groups of genes that are colocated in a set of genomes. We introduce a unified approach to...
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