人力資源與數位學習科技研究所

Abstract

　　UTCE is a platform with tools for ultrametric tree construction and tree evaluation. Phylogenetic trees can be used by biologists to describe the evolutionary relationship among of living species. Many models or tools have been proposed to construct phylogenetic trees. One of the popular models is an ultrametric tree with the assumption of a constant rate. UPGMA is one of well-known ultrametric tree building algorithms. Although UPGMA often fails to reconstruct an evolutionary tree when a molecular clock does not apply, it is suitable for some cases of clocklike data. Moreover, the assumption of a constant rate can be used by biologists to estimate or disprove initial observations or hypotheses for their research work. However, UPGMA is a heuristic algorithm and can not guarantee the constructed phylogenetic tree with minimum size. UTCE provides an efficient minimum ultrametric tree construction tool, PBBU, with a parallel branch-and-bound algorithm. The input of PBBU is a metric distance matrix or original/pre-aligned multiple DNA/protein sequences of species. It should be noted that the constructed phylogenetic tree by PBBU could not be used to reject other phylogenetic trees by UPGMA and other tools. The goal of PBBU is to give another viewpoint for biologists to observe the evolution relationship of species under the assumption of a molecular clock hypothesis and the minimum evolution principle. In addition, in UTCE, two logical methods, 3PR and 4PR,are designed to evaluate a phylogenetic tree and/or the corresponding metric distance matrix.