Composition vector approach to prokaryotic phylogeny provides an alignment-free and parameter-free method based on whole-genome data. It has also been applied to viruses and fungi. In all studied cases the inferred phylogenetic relationships agree well with taxonomic knowledge in major groupings and fine branchings. In this review article, after demonstrating its successful application to a collection of 892 genomes including 62 Archaea, 822 Bacteria and 8 Eukarya, we will outline some ongoing work towards the foundations of this new approach. (C) 2009 Elsevier B.V. All rights reserved.
[1]Fudan Univ, Dept Phys, T Life Res Ctr, Shanghai 200433, Peoples R China;
[2]Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China;
[3]Santa Fe Inst, Santa Fe, NM 87501 USA
(8.0+极速模式)