title: DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method.
abstract: CONCLUSIONS
  A number of alignment-free methods have been proposed for phylogeny reconstruction over the past two decades. But there are some long-standing challenges in these methods, including requirement of huge computer memory and CPU time, and existence of duplicate computations. In this article, we address these challenges with the idea of compressed vector, fingerprint and scalable memory management. With these ideas we developed the DLTree algorithm for efficient implementation of the dynamical language model and whole genome-based phylogenetic analysis. The DLTree algorithm was compared with other alignment-free tools, demonstrating that it is more efficient and accurate for phylogeny reconstruction.
  
  
  METHODS
  The DLTree algorithm is freely available at http://dltree.xtu.edu.cn.
  
  
  BACKGROUND
  yuzuguo@aliyun.com or yangjy@nankai.edu.cn.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wu
authors.affiliation: Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China.
authors.forename: Zu-Guo
authors.initials: ZG
authors.lastname: Yu
authors.affiliation: School of Mathematical Sciences, Nankai University, Tianjin, China.
authors.forename: Jianyi
authors.initials: J
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D010802:Phylogeny; D012984:Software; D000073336:Whole Genome Sequencing