With the advances of genomics,   phylogenetics entered a new era that is noted by the availability of   extensive collections of phylogenetic trees for thousands of individual   genes. Examples of such tree collections are the phylomes that encompass   trees for all sufficiently widespread genes in a given genome (1-4) or the   “Forest of Life” (FOL) that consists of all trees for widespread genes in a   representative set of organisms (5). It has been known since the early days   of phylogenetics that trees built on the same set of species often have   different topologies, especially when the set includes distant species, most   notably, in prokaryotes (6, 7). The availability of “forests” consisting of   numerous phylogenetic trees exacerbated the problem as an enormous diversity   of tree topologies has been revealed. The inconsistency between trees has   several major sources: 1) problems with ortholog identification caused   primarily by cryptic   paralogy, 2) various artifacts of phylogenetic analysis, such as long branch attraction (LBA),   2) horizontal gene transfer (HGT), 3) other evolutionary processes distorting   the vertical, tree-like pattern such as incomplete lineage sorting and   hybridization (1, 8-10). In order to obtain robust results in genome-level   phylogenetic analysis, for instance, to classify phylogenetic trees into clusters   with (partially) congruent topologies or to identify common trends among   multiple trees, reliable methods for comparing trees are indispensable.

随着基因组学的进步，系统发育学进入了一个新的时代，其特点是集合了成千上万个基因构建的大量系统发生树。这类树集合的例子是包含给定基因组中所有足够广泛的基因的树或“生命之林”（FOL）的系统论（基因系统发育目录），该系统论由一组特定有机体中广泛的基因的所有树组成。从系统发育早期开始，人们就知道在同一组物种上建立的系统发育树通常具有不同的拓扑结构，特别是当这组物种包括远缘物种时，尤其是在原核生物中。基于基因组数据构建的大量系统发育树，这些统发生树组成的“森林”，以及基于此的拓扑结构多样性，加剧了拓扑结构不一致的问题。发育树之间的不一致性有几个主要来源：1）主要由隐秘的旁系同源引起的直系同源鉴定问题；2）系统发育分析的各种认为偏差，如长枝吸引（LBA）；2）水平基因转移（HGT）；3）其他扭曲垂直树样模式的进化过程，如不完全支系分拣和杂交。为了在基因组水平的系统发育分析中获得可靠的结果，例如，将系统发育树分为具有（部分）一致拓扑的簇，或识别多个树之间的共同趋势，必须采用可靠的树比较方法。