Category Archives: howto

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 →

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 →

Posted in bioinformatics, genomics, howto, next generation sequencing, technical | Tagged , , , | Leave a comment

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 →

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 →

Posted in howto, R | Tagged , , , , , , , , | 3 Comments

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 →

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

Making Maps in R, volume 2: ggplots

Posted on 1 July, 2016 by Jeremy Yoder

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 →

Posted in howto, R, software | Tagged , | 6 Comments

10 simple rules for designing a scientific poster

Posted on 3 June, 2016 by Katie Everson

Conference season is upon us! Around the world, thousands of scientists face a daunting task: designing a scientific poster. It should be sleek, yet informative; eye-catching, yet professional; and most of all it should attract the attention of your future … Continue reading →

Posted in conferences, howto | Tagged , , , | 8 Comments

How to make the most out of your phylogenetic study

Posted on 14 April, 2016 by Christine Ewers-Saucedo

Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading →

Posted in data archiving, evolution, howto, phylogenetics, Uncategorized | Leave a comment

Using R to mine species data

Posted on 30 March, 2016 by Katie Everson

Many of us generate more data than we know what to do with (speaking of which: keep an eye out for the 2016 NGS Field Guide, coming soon!), so it’s easy to forget about the piles of data already at our fingertips. Research potential is … Continue reading →

Posted in howto | Tagged , , , , , | 12 Comments

The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope

Posted on 24 March, 2016 by Travis Glenn

After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading →

Posted in genomics, howto, methods, RNAseq, transcriptomics | Tagged , , , | 8 Comments