ipADMIXTURE: R package for inferring sub-population clusters based on genetic admixture

Abstract

ipADMIXTURE is an R package to infer clusters and their phylogeny based on Q matrices of genetic admixture analysis. It is the first software of its kind to infer not just only clusters, but also the hierarchy of sub-populations w.r.t. the minimum number of ancestors that split any pair of clusters apart. Since inputs of the package, Q matrices, can be obtained from well-known software (ADMIXTURE, STRUCTURE, etc.) and the Q matrices are mandatory information that are used in genetic population structure study, our package has a potential to help scientists and researchers to find deeper explanation of admixture analysis in their studies. Our package comes with a user-friendly interface to make the software accessible for everyone.

Immunogenetics and genetic variations in indigenous chicken in the tropics using SNP data

“…The K value reduces the cross-validation prediction error was then assumed as the most likely (Evanno et al, 2005) [12] . The ip ADMIXTURE R package was used to represent the results in a graph (Amornbunchornvej et al, 2020) [3] .…”

“…Admixture analysis performs maximum probability approximation of individual ancestries from multilocus SNP genotype data. A R package, ipADMIXTURE (Amornbunchornvej et al, 2020) [3] was then used to plot the ancestry of the indigenous chicken from the four zones. Admixture plots arranged the individuals according to the portion of origin they shared with other individuals.…”