BackgroundPhylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data.ResultsWe developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline.ConclusionsUsing SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Tae-Ho Lee

Hui Guo

Xiyin Wang

Changsoo Kim

Andrew H Paterson

BMC Genomics

BMC GENOMICS 是一本开放获取、同行评议的期刊，考虑关于基因组规模分析、功能基因组学和蛋白质组学各个方面的文章。BMC GENOMICS 是 BMC 系列的一部分，该系列出版专注于个人研究需求的特定主题期刊生物学和医学所有领域的社区。我们提供高效、公平和友好的同行评审服务，并致力于出版所有可靠的科学，前提是工作提供的知识有所进步。

BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genomic-scale analysis, functional genomics, and proteomics. As part of the BMC series, it focuses on specific topics that cater to the research needs of the biological and medical communities. We provide efficient, fair, and friendly peer review services and are committed to publishing all reliable science, provided that the work contributes to the advancement of knowledge.

BMC Genomics 是一本开放获取、同行评审的期刊，接受关于基因组规模分析、功能基因组学和蛋白质组学各个方面的研究文章。作为 BMC 系列的一部分，该系列专注于满足生物学和医学领域研究者的特定需求。我们提供高效、公平和友好的同行评审服务，致力于出版所有可靠的科学研究，前提是这些研究能够推动知识的进步。

Category	Quartile
生物学	2
生物学, 生物工程与应用微生物	2
生物学, 遗传学	2

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

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Journal Info

Category	Quartile
GENETICS & HEREDITY	2