echimusa/PROXYANC

PROXYANC has two novel algorithms including the correlation between observed linkage disequilibrium in an admixed population and population genetic differentiation in ancestral populations, and an optimal quadratic programming based on the linear combination of population genetic distances (FST). PROXYANC was evaluated against other methods, such as the f3 statistic using a simulated 5-way admixed population as well as real data for the local South African Coloured (SAC) population, which is also 5-way admixed. The simulation results showed that PROXYANC was a significant improvement on existing methods for multi-way admixed populations. 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 populations, as signal of natural selection. PROXYANC compute the expected maximum admixture LD from proxy ancestral populations of the admixed population. PROXYANC compute population pair-wise Fst (Genetic distance). # PROXYANC PROXYANC has two novel algorithms including the correlation between observed linkage disequilibrium in an admixed population and population genetic differentiation in ancestral populations, and an optimal quadratic programming based on the linear combination of population genetic distances (FST). PROXYANC was evaluated against other methods, such as the f3 statistic using a simulated 5-way admixed population as well as real data for the local South African Coloured (SAC) population, which is also 5-way admixed. The simulation results showed that PROXYANC was a significant improvement on existing methods for multi-way admixed populations. 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 populations, as signal of natural selection. PROXYANC compute the expected maximum admixture LD from proxy ancestral populations of the admixed population. PROXYANC compute population pair-wise Fst (Genetic distance). # PROXYANC program is free software and was developed by Dr. Emile R. Chimusa: you can redistribute it and/or modify it under the terms of …