Category Archives: methods

Crowd-sourcing natural history

What I think of as my first “real” science job was a year I spent in Pittsburgh, interning for the Western Pennsylvania Conservancy. One of my most enjoyable duties was assisting a WPC ecologist on systematic surveys of plant diversity … Continue reading

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Posted in citizen science, community, methods | 7 Comments

2014 NGS Field Guide: Resistance is Futile (mostly, at least for a while)

This year, to introduce the 2014 update to his Next Generation Sequencing Field Guide—perennially our most-accessed community resource—Travis Glenn has a bit more to say than just what goes in the tables. So here it is as a guest post! … Continue reading

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Posted in howto, methods, next generation sequencing | Leave a comment

On “triangulation” in genome scans

Guest contributor K.E. Lotterhos is a marine biologist at Wake Forest University, who studies evolutionary responses to fishing and climate change. You can find her on Twitter under then handle @dr_k_lo. A major goal of evolutionary biology is to understand the genetic … Continue reading

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Posted in adaptation, association genetics, genomics, methods, population genetics, quantitative genetics | 2 Comments

Why genetic tests are different

In yesterday’s New York Times, Kira Peikoff reported what happened when she took genetic tests for disease risks from three different providers—she got three very different results. 23andMe said my most elevated risks — about double the average — were … Continue reading

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Posted in association genetics, medicine, methods | 1 Comment

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

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Posted in adaptation, methods, population genetics, quantitative genetics, R, software, Uncategorized | 1 Comment

Getting started with Ultra Conserved Elements

Cross posted on ngcrawford.com If you attended Evolution 2013, you probably heard quite a lot of chatter about ultra conserved elements. Essentially, ultra conserved elements (UCEs) are parts of the genome that are highly conserved between different species. Although UCEs … Continue reading

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Posted in genomics, methods, phylogenetics | Leave a comment

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

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Posted in community, howto, methods, software | Leave a comment

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

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Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 13 Comments

By popular request …

The original data set of Joshua tree presence locations, which I used as an example in my post about estimating species distribution models in R, is now available for download from Dryad. Thanks to my coauthors for agreeing to share … Continue reading

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Posted in data archiving, howto, methods | Leave a 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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Posted in bioinformatics, genomics, howto, interview, methods | Leave a comment