Substack cometh, and lo it is good. (Pricing)

CLUMPAK, for model-based population structure analysis

This isn’t probably aimed at most readers, but I think it’s important to pass the word around, so, Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. An ungated version. From the abstract:

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software clumpp. Next, clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in clumpp and simplifying the comparison of clustering results across different K values. clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.

The website deploys the package as a web based application (kind of like Structure-harvester). I don’t do GUIs, but I thought I would mention it (the package is downloadable). I’ve shied away from posting admixture barplots not because I think they lack utility. Rather, over the years readers have had a hard time understanding their limitations, and tend to reify a little too much for my taste.

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