SNPViz Web-Based Version

- SNPViz can be found at
- SNPViz has a free non-commercial research-use license.
- SNPViz can run on Windows, Mac OS, and Linux using Java 7, the newest version. This program can
  run on any Internet browser except for Google Chrome for Mac because it does not support Java.
- If you are having problems running the program due to Java errors, we recommend updating Java
  (  If updating Java does not solve the problem, you will need to add to the Java exception site list. Once has been added,
  the program will be allowed to run after the appropriate security prompts. Users will first need to access
  the Java Control Panel. Within the Java Control Panel, select the Security tab and click "Edit Site List."
  Next click Add and paste into the Location box. Users then must answer yes to
  the security prompt. Mac users may need to also update the Java Development Kit and Java Runtime
- The size of a viewable and/or savable chromosome region will depend on the available memory of the
  SoyKB server and the SNP density in the region.  If SNPViz is unable to draw or save a clustering image,
  we recommend that you close the window and select a smaller chromosome region.
- To make suggestions or report problems with SNPViz, please click here.
- GWAS (31genomes)
  The GWAS dataset has SNP-array files for the 20 Glycine max chromosomes for 31 cultivated and wild
  soybean lines and the reference Williams 82.
          Information regarding this data can be found at:
          Lam HM, Xu X, Liu X, Chen W, Yang G, et al. (2010) Resequencing of 31 wild and cultivated
          soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059
- Soja
  The Soja dataset has SNP-array files for the 20 chromosomes of the Glycine soja consensus sequence
  and the reference Williams 82.  
          Information regarding this data can be found at:
          Kim MY, Lee S, Van K, Kim TH, st al. (2010) Whole-genome sequencing and intensive analysis of
          the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.
          Proc Natl Acad Sci USA 107(51):22032-7.
- To integrate datasets into one analysis, click on a dataset tab, such as GWAS (Public), and select the
  samples.  Then click on an additional dataset tab, such as Soja (Public), and select samples. Press the
  Clustering button to create a clustering image.
- Private data, such as the NAM_41 and BGI_25 datasets, can be downloaded to SoyKB by contacting
  Trupti Joshi or Dong Xu.
- We recommend that the user download the stand-alone version to input and view their datasets. The files
  for the two preloaded datasets are also included in the stand-alone download. For further details on the
  required file formats, please refer to the stand-alone README file.
- For the clustering analysis, users will have the option to choose select samples or the entire dataset.
- Annotation Information
       - Users can select gene annotations from Glymav1.0 or Glymav1.1 (
- With the three color option:
        Black = base is different from reference
        White = base is identical to reference
        Gray = missing or no data
- With the multi-color option, the IUPAC nucleotide ambiguity codes are used.
        A = Red
        G = Blue
        C = Green
        T = Yellow
        K = G/T = Dark Magenta
        M = A/C = Brown
        R = A/G = Lime
        S = C/G = Dark Red
        W = A/T = Cyan
        Y = C/T = Pink
        B = not A = Sky Blue
        D = not C = Green Yellow
        H = not G = Light Blue
        V = not T = Magenta
        N = any base = Orange
        -/. = Missing or no data = White
- A phylogeny tree is constructed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA)
  This tree can be saved as a PNG or JPEG/JPG.
- The SNP positions within the clustering tree can be saved as a text file. This text file will also include the
  gene and exon information for the haplotype region.
- A distance matrix can saved as a text file.  This distance matrix data is calculated using ClustalW.
Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. (2014) Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes. PLoS ONE 9(4): e94150. doi:10.1371/journal.pone.0094150