Category Archives: howto

Simple Gantt charts in R with ggplot2 … and Microsoft Excel

Posted on 3 January, 2019 by Jeremy Yoder

making Gantt charts is a form of self-care — Colin J. Carlson (@ColinJCarlson) November 26, 2018 If you’ve ever had to explain how all the elements of a big, multi-part project come together, you’ve probably at least considered making something … Continue reading →

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Not my problem

Posted on 30 August, 2018 by Laetitia Wilkins

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 →

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500 Queer Scientists

Posted on 23 June, 2018 by Laetitia Wilkins

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 →

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Best practices in sample naming

Posted on 30 April, 2018 by Kathryn Turner

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 →

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Posted in data archiving, fieldwork, howto, methods | Tagged , | 2 Comments

Molecular ecology, the flowchart

Posted on 2 January, 2018 by Jeremy Yoder

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 →

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Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | 1 Comment

Phylogenetic trees in R using ggtree

Posted on 8 February, 2017 by Elin Videvall

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 →

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

Handling microbial contamination in NGS data

Posted on 6 January, 2017 by Ethan Linck

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 →

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Unbalanced population sampling and STRUCTURE

Posted on 5 January, 2017 by Arun Sethuraman

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

Video Tutorial: editing R plots in Adobe Illustrator

Posted on 20 October, 2016 by Katie Everson

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 →

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On (mis)interpreting STRUCTURE/ADMIXTURE results

Posted on 5 August, 2016 by Arun Sethuraman

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 →

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