title: SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.
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.
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Lee
authors.forename: Hui
authors.initials: H
authors.lastname: Guo
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.forename: Changsoo
authors.initials: C
authors.lastname: Kim
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. paterson@plantbio.uga.edu.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D017360:Arabidopsis; D001499:Bayes Theorem; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020407:Internet; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012984:Software; D013025:Glycine max / Q000235:genetics