As part of my postdoc with Gideon Bradburd, I’m using his new software package conStruct (bioRxiv; GitHub) to analyze dozens of genomic datasets. conStruct requires three input files: 1) genetic data, 2) coordinate data (longitude in the first column, latitude in the second), and 3) a pairwise distance matrix with the same number of sites […]
Read MoreI want to use BayesAss on a large SNP dataset generated with RADseq. But I found out when I went to convert the data into the .immaq format that my favorite converter, PGDspider, would only convert the first 40 loci. I didn’t get 10,000s of loci for nothing, so that wasn’t going to work. But […]
Read MoreAt this point, who hasn’t read Patterson et al 2006 about population structure and eigenvector analysis? It’s a great paper as it introduced the EIGENSOFT package for analyzing genomic data using principal components analysis (PCA). PCA is a great way to identify both population structure and admixture relationships. For anyone that works with microsatellites, you […]
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