Category Archives: genomics

Identifying and quantifying fitness effects across loci

The following guest post by Ethan Jewett is cross-posted from the is cross-posted from the CEHG blog at Stanford. Enjoy! The degree to which similarities and differences among species are the result of natural selection, rather than genetic drift, is … Continue reading

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Posted in adaptation, genomics, population genetics, theory | 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

No reference genome? No problem! Demographic inference from genomic data in nonmodel insect populations

This guest article by Martin Sikora is cross-posted from the Computational, Evolutionary and Human Genomics blog at Stanford University. Reconstructing the demographic history of species and populations is one of the major goals of evolutionary genetics. Inferring the timing and … Continue reading

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Posted in genomics, next generation sequencing, population genetics | 2 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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Posted in bioinformatics, book review, genomics | Leave a 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

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

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

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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

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