Computer programs developed in our group

Genetic Linkage Analysis
• LD Mapping with Haplotype Data
  A program of mapping disease genes (including location and confidence interval) by using haplotypes with disease mutation and the haplotypes without disease mutation (or allele frequencies in normal population).
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• LD Mapping with Genotype Data
  This is a program to mapping the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies.
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• Multiple TDT
  a program to do the associate test (TDT type test for nuclear-family data) using several tightly linked markers simultanously
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• QSAT
  A Program for Quantitative Association Analysis
  ReadMe (PDF),    Related Paper,    Download
  
  
• Haplore
  A Program for Haplotype Reconstruction in Pedigrees
  ReadMe (PDF),    Related Paper,    Download
  
  
• Haplore (Solaris version)
  ReadMe (PDF),    Related Paper,    Download
  
  
• Haplore (Linux version)
  ReadMe (PDF),    Related Paper,    Download
  
  
Pathway Analysis and Visualization
• VitaPad
  A program to visualize and analyze pathways
  Link to the software   

Gene Array Data Analysis
• BCLUST
  A program to assess reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method
  ReadMe (PDF),    Related Paper,    Download

• QAmerge 1.0e
  Pooling replicated microarray datasets exported from QuantArray image analysis software.
  ReadMe (PDF) ,    Download

• GPmerge 4.0b
  Pooling replicated microarray datasets exported from GenePix Pro image analysis software.
  ReadMe (PDF) ,    Download

• QAnalyzer 1.0
  Statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
  ReadMe (PDF) ,    Download

• QAnalyzer 1.0 LINUX NEW!!!
  Statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
  ReadMe (PDF) ,    Download

• GProcesser 3.0 NEW!!!!
  Statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.
  ReadMe (PDF) ,    Download

• GProcesser 2.0 LINUX NEW!!!!
  Statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.
  ReadMe (PDF) ,    Download
  
  
Statistical Analysis of human nondisjunction Data
• EM based method
  An EM based algorithm to estimate genetic distances and chiasma distribution for human UPD and trisomy data.
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• HMM based method
  A Hidden Markov model based algorithm to estimate genetic distances and chiasma distribution for human UPD and trisomy data.
  Related Paper,    Download
  
  

Population Genetics
• Marker Search Power Calculation
  An R package to calculate statistical power of strategies detecting associated markers
  Readme,    Download (Zip file)    Download (Tar.gz file)
  

• Overall LD
  A program to assess the overall Linkage Disequilibrium (LD) over several markers and assess the LD between groups of markers.
  Related Paper,    Download

• Population Structure Inference
  An R package to infer population structure using genomic markers.
  Readme,    Download (Zip file)    Download (Tar.gz file)
  

Modifier Gene Analysis
• siliColony
  A program to estimate the probability that a modifier gene is responsible for the segregation of phenotypes.
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