Category Archives: software

Random drift and phenotypic evolution

Posted on 15 Oct, 2013 by peterfields

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

Posted on 24 Sep, 2013 by peterfields

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

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

Posted on 9 Sep, 2013 by peterfields

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

Posted on 3 Sep, 2013 by Jeremy Yoder

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 | 5 Comments

Want to share your code?

Posted on 27 Aug, 2013 by kimgilbert

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

Posted on 20 Aug, 2013 by Jeremy Yoder

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 , , | 71 Comments

Why do we care about population structure?

Posted on 9 Jul, 2013 by Jeremy Yoder

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 | 2 Comments

Species distribution models in R

Posted on 23 Apr, 2013 by Jeremy Yoder

Update, 20 August 2013: Many readers have requested a copy of the Joshua tree data set used as an example in this post, and I’ve finally secured permission from the coauthors of the original study to post it to Dryad. … Continue reading →

Posted in howto, R, software | Tagged , | 27 Comments

Phylogeny-aware comparisons of microbial communities – EdgePCA and Squash Clustering

Posted on 25 Mar, 2013 by hollybik

I’m jumping on the bandwagon with a blog post about this new PLoS ONE paper (taking the lead from the man in charge in my lab) because the algorithms are just so exciting: Matsen FA IV, Evans SN. (2013) Edge Principal … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, software | Tagged , , , , , , , | 1 Comment

STACKS: A program for identifying and genotyping loci with next-generation sequencing data

Posted on 15 Jan, 2013 by Mark Christie

If you have recently collected or are in the process of collecting next-generation sequencing data, then you may be wondering what the next step to working with your data will entail.  Hopefully, you have been working a little bit with … Continue reading →

Posted in methods, next generation sequencing, population genetics, software | Tagged , , | 3 Comments