Tag Archives: methods

Unbalanced population sampling and STRUCTURE

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading

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Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , | 1 Comment

Making ecology “count”: a review of the why and how of molecular ecology  

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a … Continue reading

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Posted in bioinformatics, community, community ecology, metagenomics | Tagged , , , | 1 Comment

When your programming may be inadequate to the task: new options for metagenome analysis

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading

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The trouble with PCR duplicates

The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading

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Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , | 5 Comments

Catching evolution in the act with the Singleton Density Score

A recent study led by Jonathan K. Pritchard at Stanford University brought a media storm with catchy headlines in both of the flagship scientific outlets Nature and Science News. Aside from highlighting the question of preprints without peer review being … Continue reading

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Posted in methods, mutation, population genetics, selection | Tagged , , , | 1 Comment

Geographical Heat Maps in R

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading

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Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

Genomics of Hybridization – Part II, Top three of 2015

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading

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Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment