Compact graphical representation of phylogenetic data and metadata with GraPhlAn.
Compact graphical representation of phylogenetic data and metadata with GraPhlAn.
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作者：
Asnicar F;Weingart G;Tickle TL;Huttenhower C;Segata N
基因组和宏基因组数据的日益丰富在多个分析层面带来了挑战，包括对大规模微生物及微生物群落数据以及丰富的元数据进行可视化。我们开发了GraPhlAn（图形化系统发育分析），这是一种计算工具，能够对微生物基因组和宏基因组生成高质量、简洁的可视化结果。这包括涵盖多达数千个分类群的系统发育树，并标注了从微生物群落丰度到微生物生理学或宿主及环境表型等元数据。GraPhlAn是作为一个开源的命令驱动工具开发的，以便能够轻松集成到复杂的、符合发表要求的生物信息学流程中。它既可以在本地执行，也可以通过在线的Galaxy网络应用程序执行。我们展示了几个例子，包括微生物群落的分类学和系统发育可视化、代谢功能以及生物标志物的发现，这些例子说明了GraPhlAn在现代微生物和群落基因组学中的潜力。
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.
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