中文摘要：

系统发育基因组学是利用全基因组数据构建系统发育树的新领域.全基因组数据能有效消除横向基因转移和类群间基因进化速率差异等因素对系统发育树的影响.根据所使用的全基因组数据的类型,可以将系统发育基因组学方法分为以下5类：多基因联合建树方法,基于基因含量的方法,基于基因排列信息的方法,基于序列短串含量特征信息的方法及基于代谢途径的方法.文章系统地总结了每一类方法的原理、速度、准确性、适用范围及在各个生物类群中的应用,并对系统发育基因组学的前景及面临的挑战进行了概述.

英文摘要：

Phylogenomics is a new phylogenetic field that aims to rebuild phylogenetic relationship of organisms using whole genome data. It can effectively eliminate the impact of horizontal gene transfer and variant evolutionary rates on phylogeny. According to the genome data type they are based on, these methods can be classified into five groups： mul- ti-gene based, gene content based, gene order based, K-string based, and metabolic pathway based. The mechanism, speed, accuracy, applicable range and their application of these methods are summarized. The prospects of phylogenomics and challenges that it is faced with are also discussed.