title: [A bird's eye view of the algorithms and software packages for reconstructing phylogenetic trees].
abstract: The prototype phylogenetic tree, i.e., evolutionary "tree" or "tree of life", was first conceived by Charles Darwin in his seminal book "The Origin of Species", and its reconstructions have been approached by generations of biologists ever since. In this article, we briefly reviewed the major algorithms and software packages for reconstructing phylogenetic trees. Specifically we discuss four categories of phylogeny algorithms including distance-matrix, maximum parsimony, maximum likelihood, and Bayesian framework, as well as software packages (PHYLIP, MEGA, MrBayes) based on them.
authors.affiliation: Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China. chenhongju_teacher@hotmail.com.
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Zhang
authors.forename: Chang-He
authors.initials: CH
authors.lastname: Rong
authors.forename: Yuan
authors.initials: Y
authors.lastname: He
authors.forename: Qiong
authors.initials: Q
authors.lastname: Guan
authors.forename: Bin
authors.initials: B
authors.lastname: He
authors.forename: Xing-Wen
authors.initials: XW
authors.lastname: Zhu
authors.forename: Jia-Ni
authors.initials: JN
authors.lastname: Liu
authors.forename: Hong-Ju
authors.initials: HJ
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D000818:Animals; D002965:Classification / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D012984:Software; D014714:Vertebrates / Q000145:classification* / Q000235:genetics
keywords: Bayesian framework; Distance matrix; Maximum likelihood; Maximum parsimony; Phylogenetic analysis software; Phylogenetic tree