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Category Archives: howto
Not my problem
Do American scientists know that doing research in America is a necessary step for many scientists from other parts of the world in order to get a permanent job in academia in their home country? Once in the US, these … Continue reading
500 Queer Scientists
When I heard the first time about 500 Queer Scientists (@QueerSci, #QueerSTEM) I thought for myself ‘Why do we need to support STEM scientists based on their sexual orientation?’. This is how ignorant and clumsy I am. We got sensitized … Continue reading
Posted in Action Item, career, community, howto, politics
Tagged academia, career, conduct, Homo sapiens, Knowing what I know now, society
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Best practices in sample naming
Wherein I try to save me from myself Let’s imagine a young scientist, bursting to the seems with enthusiasm and schemes to uncover the secrets of the biological world. Everything is new and she learns as she goes! Let’s call … Continue reading
Molecular ecology, the flowchart
Update: You can now buy a poster print of the Flowchart, with proceeds going to support The Molecular Ecologist! Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for … Continue reading
Phylogenetic trees in R using ggtree
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading
Posted in bioinformatics, howto, phylogenetics, R
Tagged ggtree, phylogenetics, phylogenomics, R
2 Comments
Handling microbial contamination in NGS data
Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading
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
Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE
Tagged gene flow, methods, population structure
1 Comment
Video Tutorial: editing R plots in Adobe Illustrator
Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading
Posted in howto, R
Tagged Adobe, Figures, how to, Illustrator, Plots, R, Screen Capture, Tutorial, Video
3 Comments
On (mis)interpreting STRUCTURE/ADMIXTURE results
STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading
Making Maps in R, volume 2: ggplots
The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading