Genome-wide comparison of phylogenetic   trees is becoming an increasingly common approach in evolutionary genomics,   and a variety of approaches for such comparison have been developed. In this   article we present several methods for comparative analysis of large numbers   of phylogenetic trees. To compare phylogenetic trees taking into account the   bootstrap support for each internal branch, the Boot-Split Distance (BSD)   method is introduced as an extension of the previously developed Split   Distance (SD) method for tree comparison. The BSD method implements the   straightforward idea that comparison of phylogenetic trees can be made more   robust by treating tree splits differentially depending on the bootstrap   support. Approaches are also introduced for detecting tree-like and net-like   evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the   entirety of the phylogenetic trees for conserved genes of prokaryotes. The   principal method employed for this purpose includes mapping quartets of   species onto trees to calculate the support of each quartet topology and so   to quantify the tree and net contributions to the distances between species.   We describe the applications methods used to analyze the FOL and the results   obtained with these methods. These results support the concept of the Tree of   Life (TOL) as a central evolutionary trend in the FOL as opposed to the   traditional view of the TOL as a ‘species tree’.

基于全基因组的系统发育树比较已经成为进化基因组学中一种越来越普遍的研究方法，目前已经发展出多种比较方法。本文提出了几种比较分析大量系统发生树的方法。为了比较系统发生树，考虑到每个内部节点的支持率，引入了自举分割距离（BSD）方法，作为先前开发的发育树比较分割距离（SD）方法的扩展。BSD方法秉承这样一个简单的思想，即根据自举检验支持率的不同来有区别地对待不同的分支方式，可以使系统发生树的比较更加经得起推敲。还介绍了检测生命之树林（FOL）中类树型和网型进化趋势的方法，即对原核生物保守基因的整个系统发生树进行检测。为此目的所采用的主要方法包括将物种的四分之一映射到树上，以计算每个四分之一拓扑的支持，从而量化树和网对物种之间的距离的净贡献。我们描述了应用方法来分析生命之树林和这些方法得到的结果。这些结果支持生命树（TOL）的概念，作为未来的一个中心进化趋势，而不是传统的观点，生命之树林是一个“物种树”。