Population genetics data analysis program - Powermarker v3.25

집단유전학 통계 프로그램(Population genetics data analysis program)
Powermarker  v3.25 (download)  &  manual download
(.Net framework 1.1 must installed)

Homepage =>> http://statgen.ncsu.edu/powermarker/index.html


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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

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

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

Association study

Allele test Genotype test Trend test Distance test Exact test Genotype based F-test Haplotype trend regression for binary and quantitative traits

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

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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