Category Archives: bioinformatics

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

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Totally RAD

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge: (1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts … Continue reading

Posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized | 2 Comments

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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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 | 16 Comments

Sequencer to the stars

No single person is responsible for the revolution in genetic data collection that has reshaped biology over just a handful of decades, but if you had to make a list of people deserving credit, Craig Venter’s name would be among … Continue reading

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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

How to Backup and Store your Next-Generation Sequencing (NGS) data

Congratulations!  You have recently received a file path to retrieve your hard-earned next-generation sequencing data.  You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading

Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

Q&A: Julian Catchen helps us dig into STACKS – Part II

As promised, below is part II of our interview with Julian Catchen. These questions focus more on the specifics of using stacks (i.e., user-related questions). Please see the first post if you are interested a general overview. Even more information, … Continue reading

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Q&A: Julian Catchen helps us dig into STACKS

Julian Catchen is a post-doctoral researcher at the University of Oregon, where he uses computational solutions to facilitate the analysis of next-generation sequencing data. Prior to obtaining his PhD, Julian worked for both Intel and IBM, experiences that no doubt … Continue reading

Posted in bioinformatics, genomics, howto, interview, methods | Tagged | 2 Comments

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

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

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