Category Archives: software

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

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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 | 11 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 | Leave a comment

Analytical software management for your Mac? Homebrew to the rescue!

Source: http://www.popsci.com/diy/article/2007-08/ultimate-all-one-beer-brewing-machine Much of the big processing tasks in biological research remain the domain of clusters of computer nodes, whether local or an Amazon EC2 instance, running various flavors of Linux. It is perhaps safe to say that this fact will … Continue reading

Posted in howto, software | 1 Comment

Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure

In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading

Posted in howto, population genetics, R, software, STRUCTURE | 4 Comments

Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

Making heatmaps with R for microbiome analysis

Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading

Posted in howto, microbiology, R, software | Tagged , , | 40 Comments

Why do we care about population structure?

Arun Sethuraman is 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. After nearly six years of researching population genetic structure … Continue reading

Posted in population genetics, software, STRUCTURE | Tagged | Leave a comment