Estimating differences between   phylogenetic trees is one of the fundamental questions in computational   biology. Conflicting phylogenies arise when, for example, different   phylogenetic reconstruction methods are applied to the same data set, or even   with one reconstruction method applied to multiple different genes. Gene   phylogenies may be codivergent by virtue of congruence (identical trees) or   insignificant incongruence. Otherwise, they may be significantly incongruent Maddison (1997). All of   these outcomes are fundamentally interesting. Congruence of gene trees (or   subtrees) is often considered the most desirable outcome of phylogenetic   analysis, because such a result indicates that all sequences in the clade are   orthologs (homologs derived from the same ancestral sequence without a   history of gene duplication or lateral transfer), and that discrete   monophyletic clades can be unambiguously identified, perhaps supporting novel   or previously described taxa. In contrast, gene trees that are incongruent   are often considered problematic because the precise resolution of speciation   events seems to be obscured. Thus, it would also be very useful to identify   significant incongruencies in gene trees because these represent non-canonical   evolutionary processes (e.g., Maddison and Knowles, 2006; Edwards et al.,   2007; Liu et al., 2008).

估计系统发生树间的差异是计算生物学中的一个基本问题。例如，当不同的系统发育重建方法应用于同一个数据集时，甚至一种重建方法应用于多个不同的基因时，就会产生相互冲突的系统发育树。不同的基因系统发育可能具有一致性（相同的树）或不显著的不一致性。否则，他们可能是明显不一致的（Maddison，1997）。所有这些结果从根本上来说都值得研究。基因树（或子树）的一致性通常被认为是系统发育分析最理想的结果，因为这样的结果表明，支系中的所有序列都是直系同源物（源自同一祖先序列的同源序列，没有基因重复或横向转移的历史）。并且离散的单系可以得到明确鉴定，也许支持新的未被描述过的分类群。相反，不一致的基因树通常被认为是有问题的，因为这模糊了物种形成事件的精确解析。因此，识别基因树中的显著不一致也非常有用，因为这些不一致代表非常规的进化过程（例如, Maddison and Knowles, 2006; Edwards et al., 2007; Liu et al.,   2008）。