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Summary statistics |
- Compute sample size
- Compute number of observation
- Compute allele number
- Compute availability (1 - missing
proportion)
- Compute gene diversity using biased or
unbiased version
- Compute polymorphism information content
- Compute heterozygosity
- Compute stepwise mutation index which was
defined as the maximal proportion of alleles which follow stepwise
mutation pattern
- Compute moment estimator or maximum
likelihood estimator of within-population inbreeding coefficient
- Summarize result at any level
- Bootstrap across loci to estimate
confidence intervals
- Estimate allele frequency and its variance
- Bootstrap across individual to estimate
confidence interval
- Estimate genotype frequency and allele
covariance
- Bootstrap across individual to estimate
confidence interval
- Estimate haplotype frequency using EM
algorithm
- Estimate haplotype frequency using
BisectionEM
algorithm
- Estimate haplotype frequency using TrioEM
algorithm
- Assign haplotype probabilities for each
individual
- Test Hardy-Weinberg equilibrium by
ChiSquare test
- Test Hardy-Weinberg equilibrium by
likelihood ratio test
- Test Hardy-Weinberg equilibrium by Exact
test
- Compute Hardy-Weinberg disequilibrium
statistics
- Bootstrap across individual to estimate
confidence interval for Hardy-Weinberg disequilibrium statistics
- Estimate linkage disequilibrium D
- Estimate D'
- Estimate RSquare
- Estimate population attributable risk
- Estimate proportional difference
- Estimate Yule's Q
- Estimate two-loci haplotype frequency for
computing LD statistics
- Test two-loci linkage equilibrium by
ChiSquare test
- Test two-loci linkage equilibrium by Exact
test
- Test multi-loci linkage equilibrium by
Exact test
- Prepare 2D matrix for 2D plot
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Population structure |
- Estimate population structure with
admixture
- Estimate population structure without
admixture
- Estimate classic coancestry matrix
- Estimate population specific coancestry
matrix
- Estimate classic two-level F-statistics
assuming Hardy-Weinberg equilibrium
- Estimate classic two-level F-statistics
considering inbreeding
- Estimate classic three-level F-statistics
assuming Hardy-Weinberg equilibrium
- Estimate classic three-level F-statistics
considering inbreeding
- Estimate population specific two-level
F-statistics assuming Hardy-Weinberg equilibrium
- Estimate population specific two-level
F-statistics considering inbreeding
- Bootstrap across loci to estimate
confidence interval
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Phylogenetic analysis |
- Estimate frequency from DataSet
- Estimate distance based Frequency data
using 19 different methods
- Construct UPGMA tree
- Construct NJ tree
- Bootstrap across loci to construct
multiple trees for tree consensus
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Association study |
- Allele test
- Genotype test
- Trend test
- Distance test
- Exact test
- Genotype based F-test
- Haplotype trend regression for binary and
quantitative traits
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Design |
- Choose core set of lines by allele number,
allelic diversity, allelic entropy. Selection can be done with simulated
annealing, random search or exhaustive search under general constrains
- Choose haplotype tagging markers from
haplotype data
- Choose haplotype tagging markers from
genotype data
- Choose haplotype tagging markers from trio
data
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Tools |
- Mantel test
- Contigency table analysis
- SNP identification from sequences
- Parse Structure's result
- SNP simulation under coalescence model
- SNP simulation under coalescence model
with recombination hotspots
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