Category Archives: howto

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 , , , | 7 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

Geographical Heat Maps in R

Posted on 3 March, 2016 by Arun Sethuraman

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 →

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

Quick and dirty tree building in R

Posted on 26 February, 2016 by Ethan Linck

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading →

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

2D Posterior Density Plots in R

Posted on 6 November, 2015 by Arun Sethuraman

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading →

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 1 Comment

On false positives in Isolation with Migration analyses

Posted on 19 October, 2015 by Arun Sethuraman

The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading →

Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory | Tagged , , , , , , , | 1 Comment

PCA of multilocus genotypes in R

Posted on 30 July, 2015 by Arun Sethuraman

An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 6 Comments