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

BMC Genomics

Andrew H Paterson¹  Changsoo Kim²  Xiyin Wang³  Hui Guo²  Tae-Ho Lee² 

[1] Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA;Center for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei 063009, China

关键词: Maximum likelihood;    Linkage disequilibrium;    Polymorphisms;   

Others  :  1217834
DOI  :  10.1186/1471-2164-15-162

 received in 2013-09-25, accepted in 2014-02-18,  发布年份 2014

【 摘 要 】

Background

Phylogenetic 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.

Results

We 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.

Conclusions

Using 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.

【 授权许可】

   
2014 Lee et al.; licensee BioMed Central Ltd.

【 图 表 】

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