rec-dcm-eigen reconstructing a less parsimonious but more accurate tree in shorter timerec-dcm-eigen重建一个吝啬的较少但更精确的树在较短的时间.pdfVIP

Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time 1 2 3 4 Seunghwa Kang , Jijun Tang , Stephen W. Schaeffer , David A. Bader * 1 School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America, 2 Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America, 3 Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America, 4 School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America Abstract Maximum parsimony (MP) methods aim to reconstruct the phylogeny of extant species by finding the most parsimonious evolutionary scenario using the species’ genome data. MP methods are considered to be accurate, but they are also computationally expensive especially for a large number of species. Several disk-covering methods (DCMs), which decompose the input species to multiple overlapping subgroups (or disks), have been proposed to solve the problem in a divide-and-conquer way. We design a new DCM based on the spectral method and also develop the COGNAC (Comparing Orders of Genes using Novel Algorithms and high-performance Computers) software package. COGNAC uses the new DCM to reduce the phylogenetic tree search space and selects an output tree from the reduced search space based on the MP principle. We test the new DCM using gene order data and inversion distance. The new DCM not only reduces the number of candidate tree topologies but also excludes erroneous tree topologies which can be selected by original MP methods. Initial labeling of internal genomes affects