https://popgenblog.com/tags/admixture/ Recent content in ADMIXTURE on PopGen Blog Hugo -- 0.148.2 en-us Tue, 05 Aug 2025 13:21:16 +0200 https://popgenblog.com/posts/admixture-supervised-tutorial/ Tue, 05 Aug 2025 13:21:16 +0200 https://popgenblog.com/posts/admixture-supervised-tutorial/ <p>This post is a short follow-up to the previous one on <a href="https://popgenblog.com/posts/admixture-unsupervised/">Estimating Ancestry Components Using ADMIXTURE</a>. Here, we’ll explore supervised ADMIXTURE, a mode that allows you to explicitly define ancestral populations and infer the ancestry proportions of unassigned individuals based on those references.</p> <hr> <h3 id="what-is-a-supervised-run">What Is a Supervised Run?</h3> <p>In supervised mode, ADMIXTURE skips the component discovery step and instead uses <strong>user-defined groupings</strong> to represent ancestral components. The benefit: if you already have solid candidates for reference populations, you can use them to quickly infer ancestry proportions for target or admixed individuals.</p> https://popgenblog.com/posts/admixture-unsupervised/ Sat, 02 Aug 2025 22:47:12 +0200 https://popgenblog.com/posts/admixture-unsupervised/ <p>In this post, I’ll demonstrate how to estimate ancestry proportions using one of the most widely used tools in population genetics: <a href="https://dalexander.github.io/admixture/download.html">ADMIXTURE</a>. ADMIXTURE is a model-based clustering algorithm that estimates individual ancestry proportions and ancestral allele frequencies from multilocus SNP genotypes.</p> <hr> <h3 id="preparing-the-dataset">Preparing the Dataset</h3> <p>Download the appropriate ADMIXTURE binary and either place it in your dataset directory or make it globally accessible. For this run, I included a subset of West Asian populations along with a few adjacent populations (around 150 samples in total). Linkage Disequilibrium (LD) pruning was applied beforehand. If you&rsquo;re unsure how to prune your dataset, refer to the previous post.</p>