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BMC Genomics. 2014 Feb 26;15:162. doi: 10.1186/1471-2164-15-162.

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

Author information

1
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. paterson@plantbio.uga.edu.

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.

PMID:
24571581
PMCID:
PMC3945939
DOI:
10.1186/1471-2164-15-162
[Indexed for MEDLINE]
Free PMC Article

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