1. Identification of homology relationships is essential for inferring gene functions, detecting phylogeny of gene families, discovering evolutionary history of life, and usually, is the first step of many genetic and genomic studies. However, the presence of gene duplicates, variation on evolutionary rates of homologs, fusion and fission of genes, can lead to misidentification of evolutionary relationships among homologs.
2. Here we provide a Markov clustering based method called PhyloMCL to accurately detect hierarchical orthogroups (HOGs) including orthologs and paralogs, which derived from duplications subsequent to speciation of involved species, by considering both phylogenetic relationship of organisms and effects of polyploidy events.
3. Its performance, evaluated by a list of benchmark gene families, when applying to the clustering of HOGs from 12 Metazoan genomes, reaches up to 87.8% and 83.2% on recall and precision rates respectively. Further application of PhyloMCL on classification of tens of thousands of paralogs, yielded by multiple polyploidy events during evolution of seed plants, successfully identifies the majority of in‐/out‐paralogs at different taxonomic levels.
4. Benefiting from the strategy of Markov clustering and guidance of species tree, PhyloMCL can accurately classify millions of homologous genes with affordable time, meeting the challenge of phylogenomic studies upon rapid increasing of sequenced genomes.

中文翻译：

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PhyloMCL：在系统发育关系和多倍体事件的推断的指导下，对等级正交群的准确聚类

1. 同源关系的确定对于推断基因功能，检测基因家族的系统发育，发现生命的进化史至关重要，通常，这是许多遗传和基因组研究的第一步。然而，基因重复的存在，同源物进化速率的变化，基因的融合和裂变会导致同源物之间进化关系的错误识别。
2. 在这里，我们提供了一种基于PhyloMCL的基于Markov聚类的方法，可以通过考虑生物的系统发育关系和多倍体事件的影响，准确检测包括直系同源物和旁系同源物的层次直系同源物（HOG），这些直系同源物和旁系同源物是在涉及物种物种形成后重复产生的。
3. 当将其应用于12个后生动物基因组的HOG的聚类分析时，通过一系列基准基因家族评估其性能，召回率和准确率分别达到87.8％和83.2％。PhyloMCL在种子植物进化过程中多次多倍体事件产生的数以万计的旁系同源物的分类中的进一步应用成功地鉴定了在不同分类学水平上的大多数内向/旁向同源物。
4. 得益于Markov聚类策略和物种树指导，PhyloMCL可以在可承受的时间内准确地对数百万个同源基因进行分类，从而在测序基因组快速增加的情况下满足了植物学研究的挑战。