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

By Tae-Ho Lee, Hui Guo, Xiyin Wang, Changsoo Kim, Andrew H. Paterson. BMC Genomics, 2014

458 citations recorded by the source corpus.

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. 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. 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.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/8253c35474588b2061c8937af46d0a871b2a8cbe

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Citations in the corpus

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “Users of software pipelines that automatically assemble RAD loci and generate phylogenies (Bertels et al. 2014; Lee et al. 2014) should be careful to verify that the proper models are being used for phylogeny estimation, since default settings may not be appropriate for data sets composed entirely…”