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- Title
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.
- Authors
Tae-Ho Lee; Hui Guo; Xiyin Wang; Changsoo Kim; Paterson, Andrew H.
- Abstract
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.
- Subjects
PHYLOGENY; CLADISTIC analysis; SINGLE nucleotide polymorphisms; BIOLOGICAL evolution; GENETICS; LINKAGE disequilibrium; NUCLEOTIDE sequence
- Publication
BMC Genomics, 2014, Vol 15, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-15-162