Genetic Statistics Comparison Chart
The following comparison table describes and compares the content of a series of websites that provide information and tools that are useful for undertaking a wide spectrum of analyses in genetic and genomic statistics. These include topics such as: estimation of LD; construction of Haplotypes; TDT analysis; power calculation for specific tests in genomic epidemiology etc.
| Genetic Statistics | HapMap | Seattle SNPs | Broad Institute Software | Dr David Reich's lab | Dr David Clayton's website | Tagzilla | GENESTAT (manual to choose calculation and design depending on one's need: vulgarisation) | Matthews Stephen's website | Rockefeller University Linkage software | Gonçalo's website | PEDSYS | Genetic power calculator: power calculator for the following items |
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http://www.hapmap.org/ index.html.en 
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http://pga.mbt.washington.edu
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http://www.broad.mit.edu/ tools/software.html
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http://genepath.med.harvard.edu/ ~reich
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http://www-gene.cimr.cam.ac.uk/ clayton/software
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http://tagzilla.nci.nih.gov
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http://www.genestat.org/ index.php?n=Main.HomePage
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http://stephenslab.uchicago.edu/ software.html
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http://linkage.rockefeller.edu/ soft/list.html
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http://www.sph.umich.edu/ csg/abecasis/software.html
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http://pedsys.sfbrgenetics.org/ register.html
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http://pngu.mgh.harvard.edu/ ~purcell/gpc
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| Content: Link to other pages or websites | Many separate tools: VG2, ld select, Multipop etc. | Many separate tools: Eigenstrat, Haploview, Grail etc. | Many separate tools: Ancestrymap, Eigensoft | Many separate tools: SNPHAP, STATA, SPLINK etc. | Links to: GC/GCF, Structure, EIGENSOFT etc. | Many separate tools: BIMBAM, fastPHASE, PHASE etc. | Many separate tools: BQTL, EPDT, FBAT etc. | Many separate tools: Merlin, LAMP, QTDT etc. | Many separate tools: Alterdat, Ancestor, Genomap etc. | Many separate tools: VC QTL linkage for sibship, TDT for discrete traits etc. | ||
| Tools for LD (Linkage Desequilibrium) estimation |
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| Tools for TDT (transmission Desequilibrium test: genetic assosciation) |
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| Tools for QTL (Quantitative Trait locus) or polygenic inheritance Mapping |
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| Tools for Sibship test |
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| Tools for Tag SNPs |
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| Tools for HWE: Hardy-Weinberg equilibrium |
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| Tools for SNP/ Haplotype analysis |
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| Tools for Haplotype frequency/ calculation (Phenotype prediction) |
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| Tools for Pedigree (Haplotype analysis) |
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| Tools for Population stratification (True association detection) |
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| Tools for Gene-environment interaction (continuous & dichotomous) |
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| Tools for Gene-disease association |
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| Tools for Recombination rate/ hotspot |
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