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Category Archives: software
A population genetic R-evolution
Uphill, both ways, in the snow, without shoes … quite apt when thinking of the dark days, in the not too distant past, in which a separate input file was needed for each popgen analysis in order to use a … Continue reading
Posted in howto, methods, population genetics, R, software, Uncategorized
3 Comments
haploidy, diploidy, polyploidy … not a problem
Investigating pairwise relatedness is fundamental to the characterization of the mating system and inferring genetic structure. If no pedigree exists, then relatedness is estimated from genetic markers (e.g., microsatellite loci) using method-of-moment or maximum-likelihood methods. However, not all individuals in … Continue reading
Migration Circos plots in R
We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading
Posted in bioinformatics, genomics, howto, R, software
Tagged data visualization, methods
11 Comments
Geophylogeny plots in R for Dummies
Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading
Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE
Tagged data visualization, population structure
4 Comments
The latest gadget for the molecular ecologist’s toolkit
Designing a sampling scheme to collect an organism of interest for a population genetic/genomic study can be fraught with difficulty. How best to sample? Randomly? Or, along a grid? How many individuals to sample? Thirty? Or, perhaps, the sample size … Continue reading
Admixture maps in R for Dummies
Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put … Continue reading
Posted in howto, population genetics, R, software, STRUCTURE
Tagged data visualization, population structure
14 Comments
Bayesian Markov-chain Monte Carlo in population genetics
This is a guest post by Arun Sethuraman, a postdoctoral associate with Jody Hey, studying statistical models for divergence population genetics in the Department of Biology at Temple University. You can also find him on Twitter, and on his short story blog. Prompted by the great response … Continue reading
Calculating genetic differentiation with R
As molecular ecologists, it is often necessary and useful to calculate some measure of genetic differentiation. This is often accomplished with metrics such as Wright’s Fst an or an unbiased analog (e.g., Weir & Cockerham’s Fst; G’st etc.). In addition … Continue reading
Posted in population genetics, R, software
13 Comments
Using GitHub with R and RStudio
A few weeks back, The Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading
Posted in bioinformatics, howto, R, software
29 Comments