PROXYANC implements an approach to select the best proxy ancestral populations for admixed populations. It searches for the best combination of reference populations that can minimize the genetic distance between the admixed population and all possible synthetic populations, consisting of a linear combination from reference populations. PROXYANC also computes a proxy-ancestry score by regressing a statistic for LD (at short distance < 0.25 Morgan) between a pair of SNPs in the admixed population against a weighted ancestral allele frequency differentiation. Download PROXYANC.
PROXYANANC can select AIMs based on the relationship between the observed local multi-locus linkage disequilibrium in a recently admixed population and ancestral population difference in allele frequency and based on the Kernel principal component analysis (Kernel-PCA), which is the extension of the linear PCA.
PROXYANC can identify possible unusual difference in allele frequency between pair-wise popualtions, as signal of natural selection.
PROXYANC compute the expected maximun admixture LD from proxy ancestral populations of the admixed population.
PROXYANC compute population pair-wise Fst (Genetic distance).
FractalSIM is a Python based software package, a multi-scenario whole genome-based medical population genetics simulation framework. FractalSIM, designed under the whole genome resampling simulation approach, to mimic various scenarios of population genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations, particularly those under natural selection models.
TagMix is an integrated cross-populations LD-based, haplotype-based and principal component analysis genome-wide tag SNPs selection algorithm to efficiently identify informative variants, prioritized across multi-populations of low LD and high diversity populations for custom chip array.
This approach improves the efficiency of variants and optimizing the discovery of disease-associated genetic variations.