"Data management"
 "Create new PED/MAP fileset (reordered)"
  "Preserve original allele coding" 
   <link>pom2.php?m=recode</link>  
  "Recode genotypes 11, 12 and 22 (00 missing)"
   <link>pom2.php?m=recode12</link>

 "Create a binary bED fileset" 
    <link>pom2.php?m=makebed</link>

 "Merge two PED files"
   "Output standard PED/MAP fileset"
   <link>pom2.php?m=merge&amp;p=1</link>   
   "Output a binary bED fileset"
    <link>pom2.php?m=merge&amp;p=2</link>
  
 "Extract a subset of SNPs" 
   "Output standard PED/MAP fileset"
    <link>pom2.php?m=extract&amp;p=1</link>   
   "Output a binary bED fileset"
    <link>pom2.php?m=extract&amp;p=2</link>
 
 "Exclude a subset of SNPs" 
   "Output standard PED/MAP fileset"
    <link>pom2.php?m=exclude&amp;p=1</link>   
   "Output a binary bED fileset"
    <link>pom2.php?m=exclude&amp;p=2</link>

 "Extract a subset of individuals" 
   "Output standard PED/MAP fileset"
    <link>pom2.php?m=keep&amp;p=1</link>
   "Output a binary bED fileset"
    <link>pom2.php?m=keep&amp;p=2</link>
  
 "Exclude of subset of individuals" 
   "Output standard PED/MAP fileset"
    <link>pom2.php?m=remove&amp;p=1</link> 
   "Output a binary bED fileset"
    <link>pom2.php?m=remove&amp;p=2</link>
   
 "Flip SNP strand"
   "Output standard PED/MAP fileset"
    <link>pom2.php?m=flip&amp;p=1</link>
   "Output a binary bED fileset"
    <link>pom2.php?m=flip&amp;p=2</link>
   

"Summary statistics" Type="document"
 "Missingness rates" 
  "SNP and individual missing rates" 
  <link>pom2.php?m=missing</link>
  "Test for different rates between cases and controls" 
  <link>pom2.php?m=test-missing</link>
  
 "Allele frequencies" 
  <link>pom2.php?m=freq</link>    
 
 "Hardy-Weinberg equilibrium tests"
  "Ignore phenotype" 
   <link>pom2.php?m=hardy&amp;p=1</link>    
  "Stratify by case/control statues" 
   <link>pom2.php?m=hardy&amp;p=2</link>    
  
 "Mendel error rates for nuclear family data"
   <link>pom2.php?m=mendel</link>    
 

"Population stratification and matching"
  "IBS distance-based clustering"
   "Cluster on genome-wide IBS"
   <link>pom2.php?m=cluster&amp;p=1</link>    
   "Cluster on genome-wide IBS and external matching criteria"
   <link>pom2.php?m=cluster&amp;p=2</link>    
         
  "IBD estimation (genome-wide)"
   <link>pom2.php?m=genome</link>    
        
  "Heterozygosity / inbreeding coefficients"
    <link>pom2.php?m=inbreeding</link>    
  
  "Runs of homozygosity"
    <link>pom2.php?m=homo-run-snps</link>    
    

"Linkage disequilibrium and haplotype inference"
 Pairwise r and r-squared</name>
  <link>pom2.php?m=ld-r</link> 

 "Haplotype inference"
   "Calculate haplotype frequencies"
   <link>pom2.php?m=hap&amp;p=1</link>
   "List individuals' haplotype phases"
   <link>pom2.php?m=hap&amp;p=2</link>
   "Test case/control haplotype association"
   <link>pom2.php?m=hap&amp;p=3</link>
   "Create imputed most-likely haplotype dataset"
   <link>pom2.php?m=hap&amp;p=4</link>
   

"Association analysis"
 "Single SNP analyses"
  "Population based sample"
   "Disease trait"
    "Basic allelic test" 
      "Without permutation" 
       <link>pom2.php?m=assoc&amp;p=1</link>      
      "With adaptive permutation" 
       <link>pom2.php?m=assoc&amp;p=2</link>
      "With maxT permutation" 
       <link>pom2.php?m=assoc&amp;p=3</link>
      
    "Cochran-Armitage trend test and genotypic test"
      "Without permutation" 
       <link>pom2.php?m=model&amp;p=1</link>
      "With adaptive permutation" 
       <link>pom2.php?m=model&amp;p=2</link>
      "With maxT permutation" 
       <link>pom2.php?m=model&amp;p=3</link>
      
    "Stratified/clustered sample tests"

    "Within-cluster permutation"
       <link>pom2.php?m=within-file</link>    
       
    "Cochran-Mantel-Haenszel tests"
      "SNP-disease assocation conditional on cluster"
       <link>pom2.php?m=mh1</link>          
      "SNP-cluster association conditional on disease"
       <link>pom2.php?m=mh2</link>    
     
    "Homogeneity of odds ratio tests"
       <link>pom2.php?m=homog</link>    
 
   "Quantitative trait" 
      "Without permutation" 
       <link>pom2.php?m=qt&amp;p=1</link>      
      "With adaptive permutation" 
       <link>pom2.php?m=qt&amp;p=2</link>      
      "With maxT permutation" 
       <link>pom2.php?m=qt&amp;p=3</link>
         
   "Within-cluster permutation"
     "With adaptive permutation" 
      <link>pom2.php?m=qt-within-file&amp;p=2</link>     
     "With maxT permutation" 
      <link>pom2.php?m=qt-within-file&amp;p=3</link>

  "Family-based sample"
    "Disease traits: TDT analysis" 
          "Single SNP TDT only"
          <link>pom2.php?m=tdt&amp;set=no</link>              
          "Single SNP and set-based TDT"
          <link>pom2.php?m=tdt&amp;set=true</link>    
          
    "Quantitative trait: gene-dropping permutation" 
          "Gene-drop from founders"
          <link>pom2.php?m=qtdt&amp;p=1</link>              
          "Gene-drop from parents"
          <link>pom2.php?m=qtdt&amp;p=2</link>    

"Epistatic analyses"
 "SNP x SNP epistasis"
   "Case-only analysis"
   <link>pom2.php?m=epi&amp;p=1</link>   
   "Case/control analysis"
   <link>pom2.php?m=epi&amp;p=2</link>
    
 "Gene-based epistasis"
   "Case-only analysis"
   <link>pom2.php?m=genepi&amp;p=1</link>   
   "Case/control analysis"
   <link>pom2.php?m=genepi&amp;p=2</link>