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).
  Related Paper,    Download
  
  
• 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.
  Related Paper,    Download
  
  
• Multiple TDT
  a program to do the associate test (TDT type test for nuclear-family data) using several tightly linked markers simultanously
  Related Paper,    Download
  
  
• 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.
  Related Paper,    Download

• 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
• 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.
  Download