SNPAnalyzer-2TM Freeware  
Start Page

SNPAnalyzer 2.0 is a SNP analysis software that is sequel to the SNPAnalyzer 1.0.
The current version of SNPAnalyzer is a web-based analysis tool embracing data quality check, linkage disequilibrium analysis and genetic association analysis in an integrated user interface.

FeatureMaximum data size supported
SNP/Sample Flagging 500K SNP/1000 Sample
Haplotype Estimation PLEM(200 SNP), EM(24 SNP)
LD Block Estimation 500K SNP/1000 Sample
Cross-tabulation of SNP/Haplotype 500K SNP/1000 Sample
  SNPAnalyzer-2TM Quick Start

  1. Click here to download SNPAnalyzer2 (Build 2012.11.12)
  2. Extrace downloaded zip file to anywhere you like.
  3. Run included SNPAnalyzer2.exe to start program.
  4. Click left menu "Genotype Data"
  5. Click "Open Genotype" button to load included genotype examples within example folder.
  6. Click left menu "Preprocessing", "Execute" button to flag out SNPs and samples.
  7. Click left menu "LD Blocking with...", "Execute" button to start analysis.
  8. You can change Sample combobox in the result screen to "0", "1", "M" for each sample class.
  9. Various export buttons to see internal calculation values (as text file).
  10. When you've done all with SNPAnalyzer2, you may delete SNPAnalyzer/temp directory to clean and protect your secure informations.
  11. If you have any problems, please mail me with messages in the "Log file" left menu result.
Additional important notes:
  • Old distribution using Java Webstart is deprecated ,due to recent changes in Oracle's java security rule.
    Since 2014-04-16 all users should use portable version instead.
    Calculation engine was not changed between two versions.
  • Program will auto-update itself when a new version is release.
  • Everytime SNPAnalyzer2 is executed, log will be sent back to
    Example log message:
  • Java runtime 1.7 is preinstalled within this distribution.
  • Input file name should be in alphabet characters. SNPAnalyzer2 cannot read file names in non-English alphabet.

System requirement:
  • Microsoft Windows OS (Windows XP, Windows 7,...)
  • At leasr 110 mega bytes to install

Download Example Genotype File (Download)
SNPAnalyzer2 Step by Step Tutorial [Download: PDF]
  Document & Support

Genotyoe Format (*.geno) Description

Technical Support
  • Yoo, Jinho PhD.
  • Lee, Young-Bock
  • Telephone: (Republic of Korea) 02-550-8947
    BIOAGE Co. Genomics R&D team
Citation Example:
Analysis engine files installed in your PC.

Copyright & License Statement
        Freeware, Closed-Source
  Release Info.

    SNPAnalyzer2 is changed to portable edition, removing Java Webstart

    SNPAnalyzer2 now starts using Java Webstart
    No more windows 7 UAC problems.

    Bug fix: Tagging SNP of LD analysis was not rendered correctly(shift+1)
    Cutoff value combobox is now editable (for case control analysis)

    Critical bug fix (bonferroni correction p-value)
    Bug fix: Case control analysis will crash when input file path is too long ("C:\My Document\A\B\C\...\test.geno").

    Thanks for your comments.
    Any complaint letters and feature requests are always welcome!

  Old Release Info.

2011-07-19 Workaround to overcome 'Windows 7 UAC Problem'
2008-05-01 Typo error.
2008-01-31 Initial release.
2008-02-04 Added: FDR Tabulation
2008-02-11 Added: Tutorial Document
2008-04-24 Added: HWE p-value Multiple correction. Flagging parameter Box.
2008-04-24 Enhance: Maximum Number of SNP up to 510,000 SNPs
    (for LD Blocking and Case Control Study. Warn: consumes huge memory)
2008-04-29 Bug fix: Fix Typo error genotype-format.html.
    'Column' to 'Row', vice versa.
2008-04-29 Bug fix: PLEM result is not visible when there is only 1 sample class.
2008-04-29 Bug fix: 'Out of memory' Dialog when insufficient memory to make chart.
2008-04-30 Start User Forum, Update User Manual.

+ SNPAnalyzer 2.0 Free
  + Start Page
  + Program Overview  
  + Tutorial 
  + genotype format
  + Contact (ISTECH,INC.)

+ Other Product
  + SNPAnalyzer Pro
  + SNPAnalyzer 1 Freeware 
  + SNPStudio  
  + SNPWizard  
SNPAnalyzer2TM Quick Start Page Release 2.0 α      Copyright 2008,  ISTECH