Category Archives: software

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

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Posted in bioinformatics, genomics, howto, R, software | Tagged , | Leave a comment

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 , | Leave a comment

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

Posted in genomics, methods, Molecular Ecology, the journal, natural history, pedigree, population genetics, software | 1 Comment

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 , | 3 Comments

How many markers does it take to make a dataset “genomic”?

A new paper in Ecology Letters by Matthew Fitzpatrick and Stephen Keller proposes to use some a class of statistical methods developed for understanding the distribution of species in different environments to understand the distribution of genetic variants in different … Continue reading

Posted in association genetics, genomics, next generation sequencing, population genetics, software | 6 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

Posted in methods, population genetics, software | Tagged , | 1 Comment

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 | 12 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 | 15 Comments

Random drift and phenotypic evolution

This week we have a guest post from Markku Karhunen. Markku’s research at the University of Helsinki included the development and implementation of a number of very interesting and useful population genetics methods. In his guest post Markku discusses these … Continue reading

Posted in adaptation, methods, population genetics, quantitative genetics, R, software, Uncategorized | 2 Comments

Scientific computing doesn’t have to hurt

Amy Brown handles communication and scheduling for Software Carpentry. The post title alludes to the goals of Software Carpentry, a volunteer organization whose members teach basic software skills to researchers in science, engineering, and medicine. It’s a great organization, and … Continue reading

Posted in community, howto, methods, software | 1 Comment