宏基因组中包含了环境中各种微生物的基因组信息，理论上可以得出种群结构。该如何利用宏基因组高通量测序数据分析种群结构呢？是不是要从中提取16S rRNA的数据， 组装之后使用Mothur或QIIME分析呢？
MetaPhlAn有一个不一样的想法。
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes, allowing:
- up to 25,000 reads-per-second (on one CPU) analysis speed (orders of magnitude faster compared to existing methods);
- unambiguous taxonomic assignments as the MetaPhlAn markers are clade-specific;
- accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction of reads);
- species-level resolution for bacterial and archaeal organisms;
- extensive validation of the profiling accuracy on several synthetic datasets and on thousands of real metagenomes.
它使用物种特异性的标记基因来进行分析，并且能够得到很好的种群分析结果。