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.
系统发育树又称进化树、生命树等，在达尔文的“进化论”一书中首次出现，之后系统发育树的重构被广大生物学家所接受。该文阐述了构建系统发育树的基本流程，对目前用于构建系统发育树的四类算法(距离法、最大简约法、最大似然法和贝叶斯法)进行了详细地分析和比较，并介绍了一些常用系统发育树构建和分析软件(PHYLIP、MEGA、MrBayes)的特点。
Keywords: Bayesian framework; Distance matrix; Maximum likelihood; Maximum parsimony; Phylogenetic analysis software; Phylogenetic tree.