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Category Archives: software
Visualizing Linkage Disequilibrium in R
Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading
Posted in bioinformatics, howto, population genetics, R
Tagged data visualization, genomics, population genetics
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Don't trust your data: reviewing Bioinformatics Data Skills
The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post. There is little debate on the importance of bioinformatics for the present and future of science. As molecular ecologists, we are likely more aware of this … Continue reading
F-statistics Manhattan Plots in R
Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading
Posted in bioinformatics, genomics, howto, population genetics, R, software
Tagged data visualization, genomics, Homo sapiens
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Exploring color palettes in R
How often have you had to squint at figures with unpleasant color palettes in a manuscript online or in print, and ultimately given up on distinguishing between fifty (or maybe just around 30) shades of gray? I found the RColorBrewer … Continue reading
Posted in howto, population genetics, R, software, STRUCTURE
Tagged data visualization, methods, population genetics
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Toying with eigenvectors
There are few things I enjoy more than when someone takes the time to clearly communicate a complex idea. The whole “you don’t know it until you teach it” phenomenon gives me the utmost respect for those who put effort into … Continue reading
Show me the power
Describing the patterns of genetic structure and mating system variation in presents challenges from the outset of sample collection to data analysis (see this post and this post). At the beginning of February, I had the pleasure to collaborate with Sean … Continue reading
Posted in conservation, evolution, genomics, interview, methods, population genetics, software, Uncategorized
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Comparing runs and counting K
If you are someone who has any interaction with population genetics, the letter K may cause you a distinct feeling of uneasiness. Identifying the number of distinct genetic clusters (often represented as K) in a data set is a primary component in … Continue reading
Estimating the ticks and tocks of molecular clocks
Like many undergraduate students, I learned about the linear, universal molecular clock: the homogeneous rate of nucleotide change over time. When I sat down to actually do analyses of molecular data, I was confounded by the array of options to treat DNA … Continue reading
Posted in evolution, Molecular Ecology, the journal, mutation, software
Tagged molecular clock
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The imitation game: simulating the genetics of large populations
Computational simulations of genetic data are such a powerful and flexible tool for carrying out studies in molecular ecology. Do you want to know how much explanatory power your data provides? Simulate it! Predict the future response of species to … Continue reading
SpaceMix, and a brief history of Spatial Genetics
Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, isolation by distance, methods, population structure
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